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231207_vcf_generation.sh
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231207_vcf_generation.sh
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#!/bin/bash
# Request an hour of runtime:
#SBATCH --time=60:00:00
# Define Partition
#SBATCH -p dbgap
# Use 2 nodes with 8 tasks each, for 16 MPI tasks:
#SBATCH -N 1
#SBATCH --tasks-per-node=8
#SBATCH --mem=350G
# Specify a job name:
#SBATCH -J dbGAP_vcf_generation
# Specify an output file
#SBATCH -o /dbGaP/results/iek/slurm-%j.out
#SBATCH -e /dbGaP/results/iek/slurm-%j.err
module load samtools
module load picard-tools/2.17.11
module load gatk/4.2.2.0
#for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do java -jar $PICARD AddOrReplaceReadGroups I=$i.EBV1FixMate.sorted.bam O=$i.EBV1FixMate.sorted.ReadGroups.bam RGID=$i RGSM=$i SORT_ORDER=coordinate RGPL=ILLUMINA RGPU=Run_Barcode RGLB=BLGSP VALIDATION_STRINGENCY=LENIENT & done; wait
#for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do samtools index $i.EBV1FixMate.sorted.ReadGroups.bam & done; wait
#Round1
#for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk HaplotypeCaller --java-options '-Xmx50G' -R /users/iek/data/iek/isaac_dissertation/EBV1_GRCh38.fasta -I $i.EBV1FixMate.sorted.ReadGroups.bam --standard-min-confidence-threshold-for-calling 10.0 --sample-ploidy 1 -O $i.EBV1.g.vcf.gz -ERC GVCF & done; wait
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do tabix -p vcf $i.EBV1.g.vcf.gz -ERC GVCF & done; wait
gatk GenomicsDBImport -V 2963.EBV1.g.vcf.gz -V 2964.EBV1.g.vcf.gz -V 2965.EBV1.g.vcf.gz -V 2966.EBV1.g.vcf.gz -V 2967.EBV1.g.vcf.gz -V 2968.EBV1.g.vcf.gz -V 2969.EBV1.g.vcf.gz -V 2972.EBV1.g.vcf.gz -V 2973.EBV1.g.vcf.gz -V 2974.EBV1.g.vcf.gz -V 2975.EBV1.g.vcf.gz -V 2976.EBV1.g.vcf.gz -V 2977.EBV1.g.vcf.gz -V 2979.EBV1.g.vcf.gz -V 2980.EBV1.g.vcf.gz -V 2982.EBV1.g.vcf.gz -V 2983.EBV1.g.vcf.gz -V 2984.EBV1.g.vcf.gz -V 2985.EBV1.g.vcf.gz -V 2986.EBV1.g.vcf.gz -V 2987.EBV1.g.vcf.gz -V 2988.EBV1.g.vcf.gz -V 2989.EBV1.g.vcf.gz -V 2990.EBV1.g.vcf.gz -V 2994.EBV1.g.vcf.gz -V 02cfd49c-f285-4ae7-8885-ac0f20fd4f8c_wgs_gdc_realn.EBV1.g.vcf.gz -V 08b8ce1e-63b2-444d-9f8b-7a960db4bb18_wgs_gdc_realn.EBV1.g.vcf.gz -V 0d389c84-899c-42f0-bbe3-981601ba0896_wgs_gdc_realn.EBV1.g.vcf.gz -V 1076e057-d911-41ae-a7e7-17dcb417e891_wgs_gdc_realn.EBV1.g.vcf.gz -V 117be336-5fd8-443c-aa75-3c4a4eb0548b_wgs_gdc_realn.EBV1.g.vcf.gz -V 128d236c-6b2a-46cd-a007-cda40802eaa1_wgs_gdc_realn.EBV1.g.vcf.gz -V 12906621-8ce4-4239-8b44-4c1253e91f9d_wgs_gdc_realn.EBV1.g.vcf.gz -V 1477c5fe-9ef5-467e-ad6f-60c42fd034eb_wgs_gdc_realn.EBV1.g.vcf.gz -V 15846704-e77f-4d1f-8c1b-c65b0811236f_wgs_gdc_realn.EBV1.g.vcf.gz -V 15f97967-a3f9-41fe-8641-f351b96e31e1_wgs_gdc_realn.EBV1.g.vcf.gz -V 195121f4-5a39-4096-8c62-b5b22a59eb08_wgs_gdc_realn.EBV1.g.vcf.gz -V 1d8c94ce-8324-4b2b-a394-b7d3a4cf9764_wgs_gdc_realn.EBV1.g.vcf.gz -V 1e1a632f-4f87-46f3-994b-0c25a6bae1e9_wgs_gdc_realn.EBV1.g.vcf.gz -V 23e1d555-15ab-4813-8fbe-8460eea42aa4_wgs_gdc_realn.EBV1.g.vcf.gz -V 2a493225-0598-4c59-9aae-05897e2c32eb_wgs_gdc_realn.EBV1.g.vcf.gz -V 3293b918-454d-435d-bace-b0275ec97f70_wgs_gdc_realn.EBV1.g.vcf.gz -V 34aeb8a4-6681-4b7d-b2e3-141b431e9490_wgs_gdc_realn.EBV1.g.vcf.gz -V 35b330d0-e8eb-4322-b514-735aa5e0d385_wgs_gdc_realn.EBV1.g.vcf.gz -V 35cfe5e3-4a50-4d2f-90f4-f157f2b3e5e6_wgs_gdc_realn.EBV1.g.vcf.gz -V 3711aeb1-47b6-4d82-a8ee-4d7d27b79b91_wgs_gdc_realn.EBV1.g.vcf.gz -V 3718725e-d486-4bb4-b41a-3afce1ac8eca_wgs_gdc_realn.EBV1.g.vcf.gz -V 3a8ddbdc-f477-4704-8f17-2637723b0cdb_wgs_gdc_realn.EBV1.g.vcf.gz -V 3b5da28f-8e78-4af3-a1ce-476e458d7f47_wgs_gdc_realn.EBV1.g.vcf.gz -V 3fd6e94c-211a-485a-adc6-c8315e8a34e8_wgs_gdc_realn.EBV1.g.vcf.gz -V 40ec408a-1728-4eb5-a4b6-5eb379ac2f28_wgs_gdc_realn.EBV1.g.vcf.gz -V 42fa2e74-254d-4775-a34e-a227562428db_wgs_gdc_realn.EBV1.g.vcf.gz -V 437a78da-5646-432b-b43e-b3645e73a078_wgs_gdc_realn.EBV1.g.vcf.gz -V 43c5808d-ec0f-45db-9cce-590cb755d59a_wgs_gdc_realn.EBV1.g.vcf.gz -V 44178db9-61fc-46df-b0a0-b15ed4b9b757_wgs_gdc_realn.EBV1.g.vcf.gz -V 47267de6-321d-46ed-b32a-0f708a89b497_wgs_gdc_realn.EBV1.g.vcf.gz -V 4c8eb5ae-543b-4427-aa33-b69f837dd581_wgs_gdc_realn.EBV1.g.vcf.gz -V 512001d2-2c85-47df-ac2c-a5f6601b772d_wgs_gdc_realn.EBV1.g.vcf.gz -V 529e3c76-7b24-497f-8680-c8abb5825606_wgs_gdc_realn.EBV1.g.vcf.gz -V 57fb53fd-966b-4a7e-a033-2f99e759a720_wgs_gdc_realn.EBV1.g.vcf.gz -V 5a01fe59-b463-4b9f-b760-c878c3ee2c21_wgs_gdc_realn.EBV1.g.vcf.gz -V 5b853ad2-81ea-4562-953b-597dc3b24e03_wgs_gdc_realn.EBV1.g.vcf.gz -V 5ddaf26f-a4a5-47e3-8d60-43d16cbc86cf_wgs_gdc_realn.EBV1.g.vcf.gz -V 60d70cf0-c41b-4f81-b04e-6165a41565c3_wgs_gdc_realn.EBV1.g.vcf.gz -V 610123a7-2848-452a-833a-74dc067951e9_wgs_gdc_realn.EBV1.g.vcf.gz -V 633ad88a-a50c-4555-8614-39ae0baf7fe8_wgs_gdc_realn.EBV1.g.vcf.gz -V 66e279a0-016d-4b61-b051-9d3a385d4791_wgs_gdc_realn.EBV1.g.vcf.gz -V 676f9c2a-6802-4eb3-94bb-3b9a6e0fbc87_wgs_gdc_realn.EBV1.g.vcf.gz -V 67afa5ff-11cf-413d-87e5-00e8debd5246_wgs_gdc_realn.EBV1.g.vcf.gz -V 68e608ee-d8f8-4816-b46d-c8cbed8f534e_wgs_gdc_realn.EBV1.g.vcf.gz -V 69179886-7b3c-46c3-807d-92f057f6aa03_wgs_gdc_realn.EBV1.g.vcf.gz -V 6a95177f-747d-4431-99d8-82830d4bf266_wgs_gdc_realn.EBV1.g.vcf.gz -V 6e257f50-7a7d-4a6e-ba7e-bf3406edf42f_wgs_gdc_realn.EBV1.g.vcf.gz -V 6e926a82-e703-4b55-91ad-03ef9fbbee96_wgs_gdc_realn.EBV1.g.vcf.gz -V 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8f8e821e-e860-4190-a208-53efe218bd72_wgs_gdc_realn.EBV1.g.vcf.gz -V 95d2e1ce-0333-44e7-bcbe-8534358835a7_wgs_gdc_realn.EBV1.g.vcf.gz -V 96583fbb-ac96-4663-b2d0-c33dfcf59fbd_wgs_gdc_realn.EBV1.g.vcf.gz -V 9853b66d-1f15-48a4-8e8d-856b969c6824_wgs_gdc_realn.EBV1.g.vcf.gz -V 9bbf1ef6-a137-450a-9c7f-4bb0a764274a_wgs_gdc_realn.EBV1.g.vcf.gz -V a1b90f2c-6f53-482f-9562-a0f58e797389_wgs_gdc_realn.EBV1.g.vcf.gz -V a528a3f6-f65d-4094-8126-0558c18bb911_wgs_gdc_realn.EBV1.g.vcf.gz -V a7463169-9d04-4e2d-adf9-e8ad65a3cb4d_wgs_gdc_realn.EBV1.g.vcf.gz -V a8ff6e64-053c-4b64-82a7-653c36a2bed0_wgs_gdc_realn.EBV1.g.vcf.gz -V b0b9d5a2-9612-4376-86bc-16fe79eeb9e8_wgs_gdc_realn.EBV1.g.vcf.gz -V b18892e1-a142-4fc5-bcdb-08db520877ec_wgs_gdc_realn.EBV1.g.vcf.gz -V b2e2c589-c138-43d6-a53a-f0a0407e3304_wgs_gdc_realn.EBV1.g.vcf.gz -V bbcc6048-2f8d-4d4c-a860-102d32cb8474_wgs_gdc_realn.EBV1.g.vcf.gz -V bc184aff-ea8f-4797-b965-8b1f2da31103_wgs_gdc_realn.EBV1.g.vcf.gz -V bcf14642-780b-47c9-9db3-17957198af2d_wgs_gdc_realn.EBV1.g.vcf.gz -V bd12565d-2c9a-42c9-8d3e-9083c3052f47_wgs_gdc_realn.EBV1.g.vcf.gz -V bd80e837-299d-43f1-be81-d91f3698dbfc_wgs_gdc_realn.EBV1.g.vcf.gz -V BLGSP-71-06-00015_wgs_gdc_realn.EBV1.g.vcf.gz -V BLGSP-71-06-00081_wgs_gdc_realn.EBV1.g.vcf.gz -V BLGSP-71-06-00155_wgs_gdc_realn.EBV1.g.vcf.gz -V d3b63d1c-4d18-40f3-9853-3c36a0d7412f_wgs_gdc_realn.EBV1.g.vcf.gz -V 50a50489-f2dd-48bc-bad5-9c8ee6e050cb_wgs_gdc_realn.EBV1.g.vcf.gz -V c1ecc60c-53ad-42cc-b148-5506fc1dfef3_wgs_gdc_realn.EBV1.g.vcf.gz -V c44d913b-0c32-49b0-9f86-ce77352c5593_wgs_gdc_realn.EBV1.g.vcf.gz -V c7c96abb-c2ad-4162-a734-89a57d9e8d4c_wgs_gdc_realn.EBV1.g.vcf.gz -V c91ceab1-43d4-4fbb-b311-bb5b714c22aa_wgs_gdc_realn.EBV1.g.vcf.gz -V ca8b81e1-cc22-4339-9b69-51f8cb37eac2_wgs_gdc_realn.EBV1.g.vcf.gz -V cae662b0-3232-473a-8442-dbc6c546ba91_wgs_gdc_realn.EBV1.g.vcf.gz -V cc02b433-5a9c-4639-9634-60eb6cb844d2_wgs_gdc_realn.EBV1.g.vcf.gz -V d46cc88b-abe6-4a44-bfef-1fd5ea98e838_wgs_gdc_realn.EBV1.g.vcf.gz -V d79b7114-3f1d-415f-8ac4-311ee27d2c70_wgs_gdc_realn.EBV1.g.vcf.gz -V d9d78a98-3dcd-43ed-af27-a00839840fd3_wgs_gdc_realn.EBV1.g.vcf.gz -V dbcad3c9-dcd8-4bff-be6b-22a0bdea7f1b_wgs_gdc_realn.EBV1.g.vcf.gz -V dc6138e2-3261-4515-b7f4-1e01691d2739_wgs_gdc_realn.EBV1.g.vcf.gz -V de9b62de-1750-469c-bcb3-147513d0fd34_wgs_gdc_realn.EBV1.g.vcf.gz -V df6d9dfd-635f-4d40-9971-74ec71a70d3a_wgs_gdc_realn.EBV1.g.vcf.gz -V e2b28838-0320-4000-92ac-a6308bc4db18_wgs_gdc_realn.EBV1.g.vcf.gz -V e4df8f51-8ca1-48dc-adec-957e0d697f28_wgs_gdc_realn.EBV1.g.vcf.gz -V e4f9159d-864c-4650-b1d8-c18be73463b0_wgs_gdc_realn.EBV1.g.vcf.gz -V e7d92701-64cf-436e-b0dc-ff6865ee6fe2_wgs_gdc_realn.EBV1.g.vcf.gz -V ea2ee1d3-3a70-411d-98ee-f852eda0c4ab_wgs_gdc_realn.EBV1.g.vcf.gz -V ebb5d713-c2df-4111-bdde-ea6a38615087_wgs_gdc_realn.EBV1.g.vcf.gz -V ed570a86-0714-45a7-aec0-f197e962ce59_wgs_gdc_realn.EBV1.g.vcf.gz -V f1d43ca4-06d0-43d4-b528-49ffbf1021c5_wgs_gdc_realn.EBV1.g.vcf.gz -V f8c8405c-0c51-4f71-8687-2f9f90fe3df7_wgs_gdc_realn.EBV1.g.vcf.gz -V fb40006f-8498-4e6f-a42f-893c1a4dccdc_wgs_gdc_realn.EBV1.g.vcf.gz -V fc746834-368e-4443-ad00-a143e4045796_wgs_gdc_realn.EBV1.g.vcf.gz -V ff557f39-0535-4359-b013-786959f1beed_wgs_gdc_realn.EBV1.g.vcf.gz -V --genomicsdb-workspace-path /dbGaP/results/iek/tumor_EBV1FixMate/dataset1/EBV1genomicsdbimport --tmp-dir /dbGaP/results/iek/tumor_EBV1FixMate/dataset1/tmpdir -L NC_007605
#gatk GenotypeGVCFs -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -V gendb://EBV1genomicsdbimport -O EBV1.allsamples.g.vcf.gz
#gatk SelectVariants -V EBV1.allsamples.g.vcf.gz -select-type SNP -O EBV1.allsamples.snps.vcf.gz
gatk VariantFiltration -V EBV1.allsamples.snps.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "MQ < 10.0" --filter-name "MQ10" -filter "FS > 60.0" --filter-name "FS60" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round1.snps.vcf.gz
#gatk SelectVariants -V EBV1.allsamples.g.vcf.gz -select-type INDEL -O EBV1.allsamples.indels.vcf.gz
gatk VariantFiltration -V EBV1.allsamples.indels.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "FS > 200.0" --filter-name "FS200" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round1.indels.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round1.snps.vcf.gz -O 231207.EBV1.allsamples.type1.round1.snps.filtered.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round1.indels.vcf.gz -O 231207.EBV1.allsamples.type1.round1.indels.filtered.vcf.gz
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk BaseRecalibrator -I $i.EBV1FixMate.sorted.ReadGroups.bam -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa --known-sites 231207.EBV1.allsamples.type1.round1.snps.filtered.vcf.gz --known-sites 231207.EBV1.allsamples.type1.round1.indels.filtered.vcf.gz -O $i.231207.recaldata.type1.round1.table & done; wait
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk ApplyBQSR -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -I $i.EBV1FixMate.sorted.ReadGroups.bam --bqsr-recal-file $i.231207.recaldata.type1.round1.table -O $i.231207.EBV1.bqsr1.bam & done; wait
#Round2
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk HaplotypeCaller --java-options '-Xmx50G' -R /users/iek/data/iek/isaac_dissertation/EBV1_GRCh38.fasta -I $i.231207.EBV1.bqsr1.bam --standard-min-confidence-threshold-for-calling 10.0 --sample-ploidy 1 -O $i.231207.EBV1only.round2.g.vcf.gz -ERC GVCF & done; wait
gatk GenomicsDBImport -V 2963.231207.EBV1only.round2.g.vcf.gz -V 2964.231207.EBV1only.round2.g.vcf.gz -V 2965.231207.EBV1only.round2.g.vcf.gz -V 2966.231207.EBV1only.round2.g.vcf.gz -V 2967.231207.EBV1only.round2.g.vcf.gz -V 2968.231207.EBV1only.round2.g.vcf.gz -V 2969.231207.EBV1only.round2.g.vcf.gz -V 2972.231207.EBV1only.round2.g.vcf.gz -V 2973.231207.EBV1only.round2.g.vcf.gz -V 2974.231207.EBV1only.round2.g.vcf.gz -V 2975.231207.EBV1only.round2.g.vcf.gz -V 2976.231207.EBV1only.round2.g.vcf.gz -V 2977.231207.EBV1only.round2.g.vcf.gz -V 2979.231207.EBV1only.round2.g.vcf.gz -V 2980.231207.EBV1only.round2.g.vcf.gz -V 2982.231207.EBV1only.round2.g.vcf.gz -V 2983.231207.EBV1only.round2.g.vcf.gz -V 2984.231207.EBV1only.round2.g.vcf.gz -V 2985.231207.EBV1only.round2.g.vcf.gz -V 2986.231207.EBV1only.round2.g.vcf.gz -V 2987.231207.EBV1only.round2.g.vcf.gz -V 2988.231207.EBV1only.round2.g.vcf.gz -V 2989.231207.EBV1only.round2.g.vcf.gz -V 2990.231207.EBV1only.round2.g.vcf.gz -V 2994.231207.EBV1only.round2.g.vcf.gz -V 02cfd49c-f285-4ae7-8885-ac0f20fd4f8c_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 08b8ce1e-63b2-444d-9f8b-7a960db4bb18_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 1076e057-d911-41ae-a7e7-17dcb417e891_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 117be336-5fd8-443c-aa75-3c4a4eb0548b_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 128d236c-6b2a-46cd-a007-cda40802eaa1_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 12906621-8ce4-4239-8b44-4c1253e91f9d_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 1477c5fe-9ef5-467e-ad6f-60c42fd034eb_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 15846704-e77f-4d1f-8c1b-c65b0811236f_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 195121f4-5a39-4096-8c62-b5b22a59eb08_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 1d8c94ce-8324-4b2b-a394-b7d3a4cf9764_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 1e1a632f-4f87-46f3-994b-0c25a6bae1e9_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 23e1d555-15ab-4813-8fbe-8460eea42aa4_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 2a493225-0598-4c59-9aae-05897e2c32eb_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3293b918-454d-435d-bace-b0275ec97f70_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 34aeb8a4-6681-4b7d-b2e3-141b431e9490_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 35b330d0-e8eb-4322-b514-735aa5e0d385_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 35cfe5e3-4a50-4d2f-90f4-f157f2b3e5e6_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3711aeb1-47b6-4d82-a8ee-4d7d27b79b91_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3718725e-d486-4bb4-b41a-3afce1ac8eca_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3a8ddbdc-f477-4704-8f17-2637723b0cdb_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3b5da28f-8e78-4af3-a1ce-476e458d7f47_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 3fd6e94c-211a-485a-adc6-c8315e8a34e8_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 40ec408a-1728-4eb5-a4b6-5eb379ac2f28_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 42fa2e74-254d-4775-a34e-a227562428db_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 437a78da-5646-432b-b43e-b3645e73a078_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 43c5808d-ec0f-45db-9cce-590cb755d59a_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 47267de6-321d-46ed-b32a-0f708a89b497_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 4c8eb5ae-543b-4427-aa33-b69f837dd581_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 512001d2-2c85-47df-ac2c-a5f6601b772d_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 529e3c76-7b24-497f-8680-c8abb5825606_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 57fb53fd-966b-4a7e-a033-2f99e759a720_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 5a01fe59-b463-4b9f-b760-c878c3ee2c21_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 5b853ad2-81ea-4562-953b-597dc3b24e03_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 5ddaf26f-a4a5-47e3-8d60-43d16cbc86cf_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 60d70cf0-c41b-4f81-b04e-6165a41565c3_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 610123a7-2848-452a-833a-74dc067951e9_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 633ad88a-a50c-4555-8614-39ae0baf7fe8_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 66e279a0-016d-4b61-b051-9d3a385d4791_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 676f9c2a-6802-4eb3-94bb-3b9a6e0fbc87_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 67afa5ff-11cf-413d-87e5-00e8debd5246_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 68e608ee-d8f8-4816-b46d-c8cbed8f534e_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 69179886-7b3c-46c3-807d-92f057f6aa03_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 6e257f50-7a7d-4a6e-ba7e-bf3406edf42f_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 6e926a82-e703-4b55-91ad-03ef9fbbee96_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 6fdd85b6-8185-416a-ab8b-d45f37c523ed_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 701fff05-b71a-4225-a691-15ddffdb4171_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 70454e50-eb84-4630-a095-2d1814e27fe4_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 731c7b44-04ac-4f34-a6e7-faa389c4fc03_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 742964e3-c03c-4642-9f8a-74837a5ca9e0_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 74d1aa65-36b4-497b-9ba2-f535bfc158b8_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 752697aa-fd2f-4378-ba80-88704a33b4ef_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 75b553e2-90b9-414d-9ceb-fdfeae04c0a7_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 79b0f97a-1891-4bda-8956-05e8cc841d40_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 7a45d022-0f0f-49fd-a27c-2604f1ae18e7_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 7babe5c4-59a5-4341-9661-82d3235e3c52_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 81f0fdfe-d096-4d08-8f1b-eedab0b773a5_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 87d10aec-3420-40a2-bd90-4d85c643f19b_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 8a43d359-134d-426b-b338-1eaf0456de7e_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 8f8e821e-e860-4190-a208-53efe218bd72_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 95d2e1ce-0333-44e7-bcbe-8534358835a7_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 96583fbb-ac96-4663-b2d0-c33dfcf59fbd_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 9bbf1ef6-a137-450a-9c7f-4bb0a764274a_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V a1b90f2c-6f53-482f-9562-a0f58e797389_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V a528a3f6-f65d-4094-8126-0558c18bb911_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V a7463169-9d04-4e2d-adf9-e8ad65a3cb4d_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V a8ff6e64-053c-4b64-82a7-653c36a2bed0_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V b0b9d5a2-9612-4376-86bc-16fe79eeb9e8_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V b18892e1-a142-4fc5-bcdb-08db520877ec_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V b2e2c589-c138-43d6-a53a-f0a0407e3304_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V bbcc6048-2f8d-4d4c-a860-102d32cb8474_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V bc184aff-ea8f-4797-b965-8b1f2da31103_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V bcf14642-780b-47c9-9db3-17957198af2d_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V bd12565d-2c9a-42c9-8d3e-9083c3052f47_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V bd80e837-299d-43f1-be81-d91f3698dbfc_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V BLGSP-71-06-00015_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V BLGSP-71-06-00081_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V BLGSP-71-06-00155_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V d3b63d1c-4d18-40f3-9853-3c36a0d7412f_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V 50a50489-f2dd-48bc-bad5-9c8ee6e050cb_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V c1ecc60c-53ad-42cc-b148-5506fc1dfef3_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V c44d913b-0c32-49b0-9f86-ce77352c5593_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V c7c96abb-c2ad-4162-a734-89a57d9e8d4c_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V c91ceab1-43d4-4fbb-b311-bb5b714c22aa_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V ca8b81e1-cc22-4339-9b69-51f8cb37eac2_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V cae662b0-3232-473a-8442-dbc6c546ba91_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V cc02b433-5a9c-4639-9634-60eb6cb844d2_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V d46cc88b-abe6-4a44-bfef-1fd5ea98e838_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V d79b7114-3f1d-415f-8ac4-311ee27d2c70_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V d9d78a98-3dcd-43ed-af27-a00839840fd3_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V dbcad3c9-dcd8-4bff-be6b-22a0bdea7f1b_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V dc6138e2-3261-4515-b7f4-1e01691d2739_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V de9b62de-1750-469c-bcb3-147513d0fd34_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V df6d9dfd-635f-4d40-9971-74ec71a70d3a_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V e2b28838-0320-4000-92ac-a6308bc4db18_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V e4df8f51-8ca1-48dc-adec-957e0d697f28_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V e4f9159d-864c-4650-b1d8-c18be73463b0_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V e7d92701-64cf-436e-b0dc-ff6865ee6fe2_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V ea2ee1d3-3a70-411d-98ee-f852eda0c4ab_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V ebb5d713-c2df-4111-bdde-ea6a38615087_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V ed570a86-0714-45a7-aec0-f197e962ce59_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V f1d43ca4-06d0-43d4-b528-49ffbf1021c5_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V f8c8405c-0c51-4f71-8687-2f9f90fe3df7_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V fb40006f-8498-4e6f-a42f-893c1a4dccdc_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V fc746834-368e-4443-ad00-a143e4045796_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz -V ff557f39-0535-4359-b013-786959f1beed_wgs_gdc_realn.231207.EBV1only.round2.g.vcf.gz --genomicsdb-workspace-path /dbGaP/results/iek/tumor/test/EBV1/231207_EBV1genomicsdbimport_round2 --tmp-dir /dbGaP/results/iek/tumor/test/EBV1/231207_tmpdir_round2 -L NC_007605
gatk GenotypeGVCFs -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -V gendb://231207_EBV1genomicsdbimport_round2 -O 231207.EBV1.allsamples.round2.g.vcf.gz
gatk SelectVariants -V 231207.EBV1.allsamples.round2.g.vcf.gz -select-type SNP -O 231207.EBV1.allsamples.round2.snps.vcf.gz
gatk VariantFiltration -V 231207.EBV1.allsamples.round2.snps.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "MQ < 10.0" --filter-name "MQ10" -filter "FS > 60.0" --filter-name "FS60" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round2.snps.vcf.gz
gatk SelectVariants -V 231207.EBV1.allsamples.round2.g.vcf.gz -select-type INDEL -O 231207.EBV1.allsamples.round2.indels.vcf.gz
gatk VariantFiltration -V EBV1.allsamples.round2.indels.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "FS > 200.0" --filter-name "FS200" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round2.indels.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round2.snps.vcf.gz -O 231207.EBV1.allsamples.type1.round2.snps.filtered.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round2.indels.vcf.gz -O 231207.EBV1.allsamples.type1.round2.indels.filtered.vcf.gz
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk BaseRecalibrator -I $i.EBV1FixMate.sorted.ReadGroups.bam -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa --known-sites 231207.EBV1.allsamples.type1.round2.snps.filtered.vcf.gz --known-sites 231207.EBV1.allsamples.type1.round2.indels.filtered.vcf.gz -O $i.231207.recaldata.type1.round2.table & done; wait
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk ApplyBQSR -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -I $i.EBV1FixMate.sorted.ReadGroups.bam --bqsr-recal-file $i.231207.recaldata.type1.round2.table -O $i.231207.EBV1.bqsr2.bam & done; wait
#Round3
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk HaplotypeCaller --java-options '-Xmx50G' -R /users/iek/data/iek/isaac_dissertation/EBV1_GRCh38.fasta -I $i.231207.EBV1.bqsr2.bam --standard-min-confidence-threshold-for-calling 10.0 --sample-ploidy 1 -O $i.231207.EBV1only.round3.g.vcf.gz -ERC GVCF & done; wait
gatk GenomicsDBImport -V 2963.231207.EBV1only.round3.g.vcf.gz -V 2964.231207.EBV1only.round3.g.vcf.gz -V 2965.231207.EBV1only.round3.g.vcf.gz -V 2966.231207.EBV1only.round3.g.vcf.gz -V 2967.231207.EBV1only.round3.g.vcf.gz -V 2968.231207.EBV1only.round3.g.vcf.gz -V 2969.231207.EBV1only.round3.g.vcf.gz -V 2972.231207.EBV1only.round3.g.vcf.gz -V 2973.231207.EBV1only.round3.g.vcf.gz -V 2974.231207.EBV1only.round3.g.vcf.gz -V 2975.231207.EBV1only.round3.g.vcf.gz -V 2976.231207.EBV1only.round3.g.vcf.gz -V 2977.231207.EBV1only.round3.g.vcf.gz -V 2979.231207.EBV1only.round3.g.vcf.gz -V 2980.231207.EBV1only.round3.g.vcf.gz -V 2982.231207.EBV1only.round3.g.vcf.gz -V 2983.231207.EBV1only.round3.g.vcf.gz -V 2984.231207.EBV1only.round3.g.vcf.gz -V 2985.231207.EBV1only.round3.g.vcf.gz -V 2986.231207.EBV1only.round3.g.vcf.gz -V 2987.231207.EBV1only.round3.g.vcf.gz -V 2988.231207.EBV1only.round3.g.vcf.gz -V 2989.231207.EBV1only.round3.g.vcf.gz -V 2990.231207.EBV1only.round3.g.vcf.gz -V 2994.231207.EBV1only.round3.g.vcf.gz -V 02cfd49c-f285-4ae7-8885-ac0f20fd4f8c_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 08b8ce1e-63b2-444d-9f8b-7a960db4bb18_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 1076e057-d911-41ae-a7e7-17dcb417e891_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 117be336-5fd8-443c-aa75-3c4a4eb0548b_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 128d236c-6b2a-46cd-a007-cda40802eaa1_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 12906621-8ce4-4239-8b44-4c1253e91f9d_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 1477c5fe-9ef5-467e-ad6f-60c42fd034eb_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 15846704-e77f-4d1f-8c1b-c65b0811236f_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 195121f4-5a39-4096-8c62-b5b22a59eb08_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 1d8c94ce-8324-4b2b-a394-b7d3a4cf9764_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 1e1a632f-4f87-46f3-994b-0c25a6bae1e9_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 23e1d555-15ab-4813-8fbe-8460eea42aa4_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 2a493225-0598-4c59-9aae-05897e2c32eb_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3293b918-454d-435d-bace-b0275ec97f70_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 34aeb8a4-6681-4b7d-b2e3-141b431e9490_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 35b330d0-e8eb-4322-b514-735aa5e0d385_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 35cfe5e3-4a50-4d2f-90f4-f157f2b3e5e6_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3711aeb1-47b6-4d82-a8ee-4d7d27b79b91_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3718725e-d486-4bb4-b41a-3afce1ac8eca_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3a8ddbdc-f477-4704-8f17-2637723b0cdb_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3b5da28f-8e78-4af3-a1ce-476e458d7f47_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 3fd6e94c-211a-485a-adc6-c8315e8a34e8_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 40ec408a-1728-4eb5-a4b6-5eb379ac2f28_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 42fa2e74-254d-4775-a34e-a227562428db_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 437a78da-5646-432b-b43e-b3645e73a078_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 43c5808d-ec0f-45db-9cce-590cb755d59a_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 47267de6-321d-46ed-b32a-0f708a89b497_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 4c8eb5ae-543b-4427-aa33-b69f837dd581_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 512001d2-2c85-47df-ac2c-a5f6601b772d_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 529e3c76-7b24-497f-8680-c8abb5825606_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 57fb53fd-966b-4a7e-a033-2f99e759a720_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 5a01fe59-b463-4b9f-b760-c878c3ee2c21_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 5b853ad2-81ea-4562-953b-597dc3b24e03_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 5ddaf26f-a4a5-47e3-8d60-43d16cbc86cf_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 60d70cf0-c41b-4f81-b04e-6165a41565c3_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 610123a7-2848-452a-833a-74dc067951e9_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 633ad88a-a50c-4555-8614-39ae0baf7fe8_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 66e279a0-016d-4b61-b051-9d3a385d4791_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 676f9c2a-6802-4eb3-94bb-3b9a6e0fbc87_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 67afa5ff-11cf-413d-87e5-00e8debd5246_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 68e608ee-d8f8-4816-b46d-c8cbed8f534e_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 69179886-7b3c-46c3-807d-92f057f6aa03_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 6e257f50-7a7d-4a6e-ba7e-bf3406edf42f_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 6e926a82-e703-4b55-91ad-03ef9fbbee96_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 6fdd85b6-8185-416a-ab8b-d45f37c523ed_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 701fff05-b71a-4225-a691-15ddffdb4171_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 70454e50-eb84-4630-a095-2d1814e27fe4_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 731c7b44-04ac-4f34-a6e7-faa389c4fc03_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 742964e3-c03c-4642-9f8a-74837a5ca9e0_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 74d1aa65-36b4-497b-9ba2-f535bfc158b8_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 752697aa-fd2f-4378-ba80-88704a33b4ef_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 75b553e2-90b9-414d-9ceb-fdfeae04c0a7_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 79b0f97a-1891-4bda-8956-05e8cc841d40_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 7a45d022-0f0f-49fd-a27c-2604f1ae18e7_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 7babe5c4-59a5-4341-9661-82d3235e3c52_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 81f0fdfe-d096-4d08-8f1b-eedab0b773a5_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 87d10aec-3420-40a2-bd90-4d85c643f19b_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 8a43d359-134d-426b-b338-1eaf0456de7e_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 8f8e821e-e860-4190-a208-53efe218bd72_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 95d2e1ce-0333-44e7-bcbe-8534358835a7_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 96583fbb-ac96-4663-b2d0-c33dfcf59fbd_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 9bbf1ef6-a137-450a-9c7f-4bb0a764274a_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V a1b90f2c-6f53-482f-9562-a0f58e797389_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V a528a3f6-f65d-4094-8126-0558c18bb911_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V a7463169-9d04-4e2d-adf9-e8ad65a3cb4d_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V a8ff6e64-053c-4b64-82a7-653c36a2bed0_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V b0b9d5a2-9612-4376-86bc-16fe79eeb9e8_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V b18892e1-a142-4fc5-bcdb-08db520877ec_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V b2e2c589-c138-43d6-a53a-f0a0407e3304_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V bbcc6048-2f8d-4d4c-a860-102d32cb8474_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V bc184aff-ea8f-4797-b965-8b1f2da31103_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V bcf14642-780b-47c9-9db3-17957198af2d_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V bd12565d-2c9a-42c9-8d3e-9083c3052f47_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V bd80e837-299d-43f1-be81-d91f3698dbfc_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V BLGSP-71-06-00015_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V BLGSP-71-06-00081_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V BLGSP-71-06-00155_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V d3b63d1c-4d18-40f3-9853-3c36a0d7412f_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V 50a50489-f2dd-48bc-bad5-9c8ee6e050cb_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V c1ecc60c-53ad-42cc-b148-5506fc1dfef3_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V c44d913b-0c32-49b0-9f86-ce77352c5593_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V c7c96abb-c2ad-4162-a734-89a57d9e8d4c_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V c91ceab1-43d4-4fbb-b311-bb5b714c22aa_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V ca8b81e1-cc22-4339-9b69-51f8cb37eac2_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V cae662b0-3232-473a-8442-dbc6c546ba91_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V cc02b433-5a9c-4639-9634-60eb6cb844d2_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V d46cc88b-abe6-4a44-bfef-1fd5ea98e838_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V d79b7114-3f1d-415f-8ac4-311ee27d2c70_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V d9d78a98-3dcd-43ed-af27-a00839840fd3_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V dbcad3c9-dcd8-4bff-be6b-22a0bdea7f1b_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V dc6138e2-3261-4515-b7f4-1e01691d2739_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V de9b62de-1750-469c-bcb3-147513d0fd34_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V df6d9dfd-635f-4d40-9971-74ec71a70d3a_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V e2b28838-0320-4000-92ac-a6308bc4db18_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V e4df8f51-8ca1-48dc-adec-957e0d697f28_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V e4f9159d-864c-4650-b1d8-c18be73463b0_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V e7d92701-64cf-436e-b0dc-ff6865ee6fe2_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V ea2ee1d3-3a70-411d-98ee-f852eda0c4ab_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V ebb5d713-c2df-4111-bdde-ea6a38615087_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V ed570a86-0714-45a7-aec0-f197e962ce59_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V f1d43ca4-06d0-43d4-b528-49ffbf1021c5_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V f8c8405c-0c51-4f71-8687-2f9f90fe3df7_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V fb40006f-8498-4e6f-a42f-893c1a4dccdc_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V fc746834-368e-4443-ad00-a143e4045796_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz -V ff557f39-0535-4359-b013-786959f1beed_wgs_gdc_realn.231207.EBV1only.round3.g.vcf.gz --genomicsdb-workspace-path 231207_EBV1genomicsdbimport_round3 --tmp-dir 231207_tmpdir_round3 -L NC_007605
gatk GenotypeGVCFs -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -V gendb://231207_EBV1genomicsdbimport_round3 -O 231207.EBV1.allsamples.round3.g.vcf.gz
gatk SelectVariants -V 231207.EBV1.allsamples.round3.g.vcf.gz -select-type SNP -O 231207.EBV1.allsamples.round3.snps.vcf.gz
gatk VariantFiltration -V 231207.EBV1.allsamples.round3.snps.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "MQ < 10.0" --filter-name "MQ40" -filter "FS > 60.0" --filter-name "FS60" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round3.snps.vcf.gz
gatk SelectVariants -V 231207.EBV1.allsamples.round3.g.vcf.gz -select-type INDEL -O 231207.EBV1.allsamples.round3.indels.vcf.gz
gatk VariantFiltration -V 231207.EBV1.allsamples.round3.indels.vcf.gz -filter "QD < 2.0" --filter-name "QD2" -filter "FS > 200.0" --filter-name "FS200" -filter "DP < 5" --filter-name "DP5" -O 231207.EBV1.allsamples.type1.round3.indels.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round3.snps.vcf.gz -O 231207.EBV1.allsamples.type1.round3.snps.filtered.vcf.gz
gatk SelectVariants --exclude-filtered -V 231207.EBV1.allsamples.type1.round3.indels.vcf.gz -O 231207.EBV1.allsamples.type1.round3.indels.filtered.vcf.gz
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk BaseRecalibrator -I $i.EBV1FixMate.sorted.ReadGroups.bam -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa --known-sites 231207.EBV1.allsamples.type1.round3.snps.filtered.vcf.gz --known-sites 231207.EBV1.allsamples.type1.round3.indels.filtered.vcf.gz -O $i.231207.recaldata.type1.round3.table & done; wait
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk ApplyBQSR -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -I $i.EBV1FixMate.sorted.ReadGroups.bam --bqsr-recal-file $i.231207.recaldata.type1.round3.table -O $i.231207.EBV1.bqsr3.bam & done; wait
#Round4
for i in $(ls -1 *.EBV1FixMate.sorted.bam | sed 's/.EBV1FixMate.sorted.bam//'); do gatk HaplotypeCaller --java-options '-Xmx50G' -R /users/iek/data/iek/isaac_dissertation/EBV1_GRCh38.fasta -I $i.231207.EBV1.bqsr3.bam --standard-min-confidence-threshold-for-calling 10.0 --sample-ploidy 1 -O $i.231207.EBV1only.round4.g.vcf.gz -ERC GVCF & done; wait
gatk GenomicsDBImport -V 2963.231207.EBV1only.round4.g.vcf.gz -V 2964.231207.EBV1only.round4.g.vcf.gz -V 2965.231207.EBV1only.round4.g.vcf.gz -V 2966.231207.EBV1only.round4.g.vcf.gz -V 2967.231207.EBV1only.round4.g.vcf.gz -V 2968.231207.EBV1only.round4.g.vcf.gz -V 2969.231207.EBV1only.round4.g.vcf.gz -V 2972.231207.EBV1only.round4.g.vcf.gz -V 2973.231207.EBV1only.round4.g.vcf.gz -V 2974.231207.EBV1only.round4.g.vcf.gz -V 2975.231207.EBV1only.round4.g.vcf.gz -V 2976.231207.EBV1only.round4.g.vcf.gz -V 2977.231207.EBV1only.round4.g.vcf.gz -V 2979.231207.EBV1only.round4.g.vcf.gz -V 2980.231207.EBV1only.round4.g.vcf.gz -V 2982.231207.EBV1only.round4.g.vcf.gz -V 2983.231207.EBV1only.round4.g.vcf.gz -V 2984.231207.EBV1only.round4.g.vcf.gz -V 2985.231207.EBV1only.round4.g.vcf.gz -V 2986.231207.EBV1only.round4.g.vcf.gz -V 2987.231207.EBV1only.round4.g.vcf.gz -V 2988.231207.EBV1only.round4.g.vcf.gz -V 2989.231207.EBV1only.round4.g.vcf.gz -V 2990.231207.EBV1only.round4.g.vcf.gz -V 2994.231207.EBV1only.round4.g.vcf.gz -V 02cfd49c-f285-4ae7-8885-ac0f20fd4f8c_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 08b8ce1e-63b2-444d-9f8b-7a960db4bb18_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 1076e057-d911-41ae-a7e7-17dcb417e891_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 117be336-5fd8-443c-aa75-3c4a4eb0548b_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 128d236c-6b2a-46cd-a007-cda40802eaa1_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 12906621-8ce4-4239-8b44-4c1253e91f9d_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 1477c5fe-9ef5-467e-ad6f-60c42fd034eb_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 15846704-e77f-4d1f-8c1b-c65b0811236f_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 195121f4-5a39-4096-8c62-b5b22a59eb08_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 1d8c94ce-8324-4b2b-a394-b7d3a4cf9764_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 1e1a632f-4f87-46f3-994b-0c25a6bae1e9_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 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b0b9d5a2-9612-4376-86bc-16fe79eeb9e8_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V b18892e1-a142-4fc5-bcdb-08db520877ec_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V b2e2c589-c138-43d6-a53a-f0a0407e3304_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V bbcc6048-2f8d-4d4c-a860-102d32cb8474_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V bc184aff-ea8f-4797-b965-8b1f2da31103_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V bcf14642-780b-47c9-9db3-17957198af2d_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V bd12565d-2c9a-42c9-8d3e-9083c3052f47_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V bd80e837-299d-43f1-be81-d91f3698dbfc_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V BLGSP-71-06-00015_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V BLGSP-71-06-00081_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V BLGSP-71-06-00155_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V d3b63d1c-4d18-40f3-9853-3c36a0d7412f_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V 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dbcad3c9-dcd8-4bff-be6b-22a0bdea7f1b_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V dc6138e2-3261-4515-b7f4-1e01691d2739_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V de9b62de-1750-469c-bcb3-147513d0fd34_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V df6d9dfd-635f-4d40-9971-74ec71a70d3a_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V e2b28838-0320-4000-92ac-a6308bc4db18_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V e4df8f51-8ca1-48dc-adec-957e0d697f28_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V e4f9159d-864c-4650-b1d8-c18be73463b0_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V e7d92701-64cf-436e-b0dc-ff6865ee6fe2_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V ea2ee1d3-3a70-411d-98ee-f852eda0c4ab_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V ebb5d713-c2df-4111-bdde-ea6a38615087_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V ed570a86-0714-45a7-aec0-f197e962ce59_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V f1d43ca4-06d0-43d4-b528-49ffbf1021c5_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V f8c8405c-0c51-4f71-8687-2f9f90fe3df7_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V fb40006f-8498-4e6f-a42f-893c1a4dccdc_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V fc746834-368e-4443-ad00-a143e4045796_wgs_gdc_realn.231207.EBV1only.round4.g.vcf.gz -V ff557f39-0535-4359-b013-786959f1beed_wgs_gdc_realn --genomicsdb-workspace-path /dbGaP/results/iek/tumor/test/EBV1/231207_EBV1genomicsdbimport_round4 --tmp-dir /dbGaP/results/iek/tumor/test/EBV1/231207_tmpdir_round4 -L NC_007605
gatk GenotypeGVCFs -R /users/iek/data/iek/isaac_dissertation/EBV1_NC_007605.fa -V gendb://231207_EBV1genomicsdbimport_round4 -O 231207.EBV1.allsamples.round4.g.vcf.gz