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14. Index BAM files
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14. Index BAM files
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#!/bin/bash
#SBATCH -n 8
#SBATCH --job-name=Bamtools_indexMerged
#SBATCH -t 0-4:0
#SBATCH -A mwilsons
#SBATCH -o slurm.Bamtools_indexMerged.out
#SBATCH -e slurm.Bamtools_indexMerged.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected]
#--------------------------
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to directory and load programs
#--------------------------
cd /scratch/kcolney/cancerCellLines_Haynes/2_data/BAM/
module load bamtools/2.4.0
#--------------------------
# 3. BAMtools index split BAMs
#--------------------------
bamtools index -in KH10_S2.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH11_S3.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH12_S4.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH13_S5.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH14_S6.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH15_S7.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH16_S8.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH17_S9.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH18_S9.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH19_S10.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH1_S1.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH20_S10.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH21_S11.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH22_S11.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH23_S12.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH24_S12.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH2_S2.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH3_S3.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH4_S4.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH5_S5.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH6_S6.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH7_S7.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH8_S8.sort.markdup.readgrps.split.merge.bam
bamtools index -in KH9_S1.sort.markdup.readgrps.split.merge.bam
#--------------------------
# 4. end timer
#--------------------------
date