updated README

HKU-BAL · Oct 11, 2024 · 3915cff · 3915cff
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Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -400,12 +400,12 @@ Particularly, if the `--panel_of_normals` option is not specified, the four defa
 
 In addition, we recommend using `--panel_of_normals_require_allele_matching` option that takes comma separated booleans to indicate whether to require allele matching for each of the PoNs given in `--panel_of_normals`. By default, allele matching is enabled when using germline variants sources (e.g., gnomAD, dbSNP) for non-somatic tagging, and is disabled when using panels (e.g., 1000G PoN, CoLoRSdb).
 
-| Default PoNs |                                                     URL                                                      | Source |                                                    Source URL                                                    |        Last visited         | Total #Variants |        Filters         | #Variants used for tagging | Remaining Columns in the input   |
-|:------------:|:------------------------------------------------------------------------------------------------------------:|:------:|:----------------------------------------------------------------------------------------------------------------:|:---------------------------:|:---------------:|:----------------------:|:--------------------------:|:--------------------------------:|
-|    PoN 1     |              http://www.bio8.cs.hku.hk/clairs-to/databases/gnomad.r2.1.af-ge-0.001.sites.vcf.gz              |  GATK gnomAD  |            https://storage.googleapis.com/gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz            |  July 10, 2023 PM10∶34∶07   |   268,225,276   | Sites with AF ≥ 0.001  |         35,551,905         |     #CHROM  POS ID  REF ALT      |
-|    PoN 2     |              http://www.bio8.cs.hku.hk/clairs-to/databases/dbsnp.b138.non-somatic.sites.vcf.gz               |  GATK dbSNP  | https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf |  July 10, 2023 PM10∶42∶22   |   60,691,395    |   Non-Somatic sites    |         60,683,019         |     #CHROM  POS ID  REF ALT      |
-|    PoN 3     |                     http://www.bio8.cs.hku.hk/clairs-to/databases/1000g-pon.sites.vcf.gz                     |  GATK 1000G PoN  |              https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz               |  July 10, 2023 PM10∶31∶32   |    2,609,566    |       All sites        |         2,609,566          |     #CHROM  POS ID  REF ALT      |
-|    PoN 4     | http://www.bio8.cs.hku.hk/clairs-to/databases/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.af-ge-0.001.vcf.gz  |  GATK 1000G PoN  |           https://zenodo.org/records/13145123/files/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.vcf.gz            | August 21, 2024 PM10∶36∶10  |   49,550,902    | Sites with AF ≥ 0.001  |         41,175,834         |     #CHROM  POS ID  REF ALT      |
+| Default PoNs |                                                     URL                                                      |                         Source                         |                                                    Source URL                                                    |        Last visited         | Total #Variants |        Filters         | #Variants used for tagging | Remaining Columns in the input   |
+|:------------:|:------------------------------------------------------------------------------------------------------------:|:------------------------------------------------------:|:----------------------------------------------------------------------------------------------------------------:|:---------------------------:|:---------------:|:----------------------:|:--------------------------:|:--------------------------------:|
+|    PoN 1     |              http://www.bio8.cs.hku.hk/clairs-to/databases/gnomad.r2.1.af-ge-0.001.sites.vcf.gz              |                      GATK gnomAD                       |            https://storage.googleapis.com/gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz            |  July 10, 2023 PM10∶34∶07   |   268,225,276   | Sites with AF ≥ 0.001  |         35,551,905         |     #CHROM  POS ID  REF ALT      |
+|    PoN 2     |              http://www.bio8.cs.hku.hk/clairs-to/databases/dbsnp.b138.non-somatic.sites.vcf.gz               |                       GATK dbSNP                       | https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf |  July 10, 2023 PM10∶42∶22   |   60,691,395    |   Non-Somatic sites    |         60,683,019         |     #CHROM  POS ID  REF ALT      |
+|    PoN 3     |                     http://www.bio8.cs.hku.hk/clairs-to/databases/1000g-pon.sites.vcf.gz                     |                     GATK 1000G PoN                     |              https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz               |  July 10, 2023 PM10∶31∶32   |    2,609,566    |       All sites        |         2,609,566          |     #CHROM  POS ID  REF ALT      |
+|    PoN 4     | http://www.bio8.cs.hku.hk/clairs-to/databases/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.af-ge-0.001.vcf.gz  | Consortium of Long Read Sequencing Database (CoLoRSdb) |           https://zenodo.org/records/13145123/files/CoLoRSdb.GRCh38.v1.1.0.deepvariant.glnexus.vcf.gz            | August 21, 2024 PM10∶36∶10  |   49,550,902    | Sites with AF ≥ 0.001  |         41,175,834         |     #CHROM  POS ID  REF ALT      |
 
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