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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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  • ModelSegments not reading allelic counts file Answered
    • Ross Jackson
    • May 11, 2022 06:36
    0 votes 1 comment
  • 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
  • Contig chr1_KQ031383v1_fix not present in the sequence dictionary Answered
    • zzh
    • March 29, 2022 03:39
    0 votes 5 comments
  • FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag Answered
    • Francesco Mazzarotto
    • March 23, 2022 14:16
    0 votes 9 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
  • 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
  • FilterMutectCalls, --distance-on-haplotype and variants filtered for haplotype Answered
    • ElenaGrassi
    • February 03, 2022 10:28
    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
  • 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
  • Baserecalibarator error: half of the files worked without any error Answered
    • Huma Shehwana
    • January 17, 2022 12:19
    0 votes 1 comment
  • Mutect2 unexpected false negative due to changes in smith-waterman parameters? Answered
    • myourshaw
    • January 14, 2022 20:14
    • Edited
    0 votes 3 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
  • mutect2.bam could not find the mutation, but bqsr found the mutation Answered
    • cjz
    • December 09, 2021 08:04
    0 votes 1 comment
  • mutect2 genotyping wrong? Answered
    • Jeffcgen2000
    • December 02, 2021 22:54
    0 votes 1 comment
  • 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
  • Error while running ModelSegments Answered
    • onurerdoganmd
    • November 09, 2021 20:52
    0 votes 3 comments
  • Mutect2 Funcotator interval error Answered
    • Elise Valkanas (she/her)
    • November 09, 2021 15:39
    • Edited
    0 votes 5 comments
  • Called Somatic Mutations High Frequency of C>A SNVs Answered
    • Jeremy Huang
    • November 04, 2021 14:46
    • Edited
    0 votes 6 comments
  • empty pon vcf file Answered
    • Lait
    • November 03, 2021 14:32
    1 vote 1 comment
  • Funconator's ignore-filtered-variants is not a recognized option Answered
    • Stephen Chung
    • October 26, 2021 15:16
    0 votes 1 comment
  • missing file: Callset.json , when creating PON Answered
    • Lait
    • October 22, 2021 10:13
    0 votes 3 comments
  • MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true does not add DS and DI tags in the output BAM file Answered
    • Adeline Morez
    • October 22, 2021 09:44
    • Edited
    0 votes 3 comments
  • SAMException: Value was put into PairInfoMap more than once Answered
    • Mohammad Tanhaemami
    • October 21, 2021 13:43
    • Edited
    0 votes 5 comments
  • Why do I see a variant called by mutect2 in my matched-normal sample when checking the results? Answered
    • Jenifer
    • October 20, 2021 11:34
    • Edited
    0 votes 10 comments
  • Mutect2 calls long deletion with absolutely zero read support Answered
    • Brian Wiley
    • October 19, 2021 00:53
    0 votes 1 comment
  • Deletion is split into two deletions Answered
    • Maximilian Dörrbecker
    • October 05, 2021 08:07
    0 votes 1 comment
  • Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries? Answered
    • Ruiqiao Bai
    • September 12, 2021 01:06
    0 votes 12 comments
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Incorrect Annotation from Funcotator Answered
    • Hanbing Song
    • August 26, 2021 00:49
    0 votes 5 comments
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