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Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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  • Panel of normal issue
    • Simon Haefliger
    • June 29, 2022 08:04
    0 votes 2 comments
  • Increased number of false positives in Mutect2 GATK 4.1.7.0
    • registered_user
    • May 18, 2020 12:53
    • Edited
    0 votes 14 comments
  • Empty final PON vcf file from 7 samples Answered
    • Yun Yu
    • January 04, 2021 08:42
    0 votes 18 comments
  • Funcotator: Unable to open SQLite DB for COSMIC Answered
    • AB
    • June 03, 2022 19:23
    • Edited
    0 votes 7 comments
  • The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered
    • Ce Wang
    • May 25, 2021 06:08
    • Edited
    0 votes 19 comments
  • FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered
    • Francesco Mazzarotto
    • March 23, 2022 14:16
    0 votes 9 comments
  • ModelSegments not reading allelic counts file Answered
    • Ross Jackson
    • May 11, 2022 06:36
    0 votes 1 comment
  • Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz
    • Saya Rene Dennis
    • April 27, 2022 22:37
    0 votes 3 comments
  • ModelSegments - java.lang.IllegalArgumentException: Metadata of the allelic counts and the segments do not match Answered
    • Tony Tan
    • April 19, 2022 02:48
    • Edited
    0 votes 3 comments
  • Error in building panel of normal in somatic copy number variation calling Answered
    • Lei Yu
    • April 04, 2022 21:55
    0 votes 4 comments
  • In Mutect2 force-calling allele via --alleles does not force-call the allele Answered
    • Rahul Gupta
    • February 04, 2022 17:13
    • Edited
    0 votes 14 comments
  • Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered
    • zzh
    • March 29, 2022 03:39
    0 votes 5 comments
  • How to create Panel of Normals?
    • Tanay Biswas
    • March 25, 2022 13:16
    • Edited
    0 votes 7 comments
  • A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file Answered
    • jesus ix ballote
    • March 04, 2022 20:34
    0 votes 7 comments
  • Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered
    • yqiu
    • January 06, 2022 00:13
    • Edited
    1 vote 13 comments
  • FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered
    • ElenaGrassi
    • February 03, 2022 10:28
    0 votes 9 comments
  • GenomicsDBImport error: USER ERROR has occurred: Duplicate sample: 1. Sample was found in both file: Completed
    • Yuna Son
    • August 08, 2020 02:58
    0 votes 9 comments
  • Read-orientation filter removes tens of thousands of somatic variants after FilterMutectCalls Answered
    • Santiago Sanchez
    • January 25, 2022 18:21
    0 votes 6 comments
  • Mutect2 java.lang.NullPointerException Answered
    • Saskia
    • September 25, 2020 15:01
    0 votes 7 comments
  • Mutect2 unexpected false negative due to changes in smith-waterman parameters? Answered
    • myourshaw
    • January 14, 2022 20:14
    • Edited
    0 votes 3 comments
  • af-only-gnomad.raw.sites.b37.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file Answered
    • linouhao
    • January 19, 2022 02:05
    0 votes 3 comments
  • Mutect2 Funcotator interval error Answered
    • Elise Valkanas (she/her)
    • November 09, 2021 15:39
    • Edited
    0 votes 5 comments
  • Baserecalibarator error: half of the files worked without any error Answered
    • Huma Shehwana
    • January 17, 2022 12:19
    0 votes 1 comment
  • Mutect2 missing a low AF known deletion
    • yingchen69
    • January 12, 2022 16:50
    0 votes 4 comments
  • GenomicsDBImport: are all intervals being processed or is there an error? Answered
    • ISmolicz
    • November 21, 2020 17:55
    0 votes 4 comments
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Broad hg19 TWIST interval list Answered
    • Tejas Jammihal
    • January 20, 2021 17:14
    1 vote 4 comments
  • mutect2.bam could not find the mutation, but bqsr found the mutation Answered
    • cjz
    • December 09, 2021 08:04
    0 votes 1 comment
  • GGA-mode gives PASS tag while the site failed in the normal workflow
    • xiucz
    • November 16, 2021 03:22
    • Edited
    0 votes 13 comments
  • How to decrease the likelihood threshold for a candidate haplotype to be called as a genotype in Mutect2 Answered
    • Yussanne Ma
    • November 19, 2021 02:58
    0 votes 9 comments
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