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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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Documentation Questions

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  • Germline CNV vs HaplotypeCaller/indels
    • Heba B abusamra
    • September 03, 2020 06:02
    0 votes 1 comment
  • ASEReadCounter count each read only once or not
    • Qingnan Liang
    • September 02, 2020 00:38
    0 votes 1 comment
  • error-handling-end-exit-codes-in-gatk
    • Kshama Aswath
    • August 19, 2020 18:50
    0 votes 1 comment
  • What do the two different minimum base quality filters do in Mutect2?
    • Nick Bernstein
    • August 14, 2020 21:25
    0 votes 3 comments
  • Funcotator misses many Cosmic fields - update possible?
    • Tjitske de Vries
    • August 13, 2020 08:41
    0 votes 1 comment
  • panel of normal hg19 version Answered
    • 김성윤
    • August 11, 2020 07:38
    0 votes 1 comment
  • The base of logarithm for VQSLOD
    • Edward David
    • August 04, 2020 21:36
    0 votes 1 comment
  • GATK-CollectVariantCallingMetrics - regarding more information
    • Krithika_Subramanian
    • August 04, 2020 14:33
    0 votes 1 comment
  • Germline Resouce Answered
    • happyhihello
    • July 31, 2020 17:23
    1 vote 3 comments
  • Create Somatic PON threshold Answered
    • Pedro Miguel Raposo
    • July 31, 2020 14:53
    0 votes 1 comment
  • Map reads to a reference with alternate contigs like GRCH38 using GATK4
    • neethukrishna Kausthubham
    • July 29, 2020 10:14
    0 votes 3 comments
  • Mulitple mapped reads in germline CNV caller (GermlineCNVCaller) Answered
    • chrl
    • July 29, 2020 07:50
    0 votes 1 comment
  • Should we run MarkDuplicates on PCR-Free Libraries made using PCR-Free Kits to take care of Optical Duplicates ?
    • rohit satyam
    • July 28, 2020 20:28
    • Edited
    0 votes 2 comments
  • After SNPs and INDELs are extracted, can they be recombined later? Answered
    • Daniel Westcott
    • July 23, 2020 23:09
    0 votes 1 comment
  • Mutect2 call some structural variants as indel ,how to filter it? Answered
    • zouxuan
    • July 17, 2020 08:30
    0 votes 3 comments
  • Use of VQSR when joint calling samples from targeted and whole genome sequencing
    • Scott Frodsham
    • July 02, 2020 17:40
    0 votes 1 comment
  • GATK CNV interpret Segment_Mean and MEAN_LOG2_COPY_RATIO Answered
    • lzhan140
    • June 24, 2020 23:04
    0 votes 3 comments
  • gCNV
    • Sabrina Camp
    • June 24, 2020 10:13
    2 votes 1 comment
  • Questions Regarding VCF Files Found in hg38 Public Resource Bundle
    • Sara Coder
    • June 17, 2020 23:18
    0 votes 4 comments
  • Output of PossibleDeNovo Answered
    • Sanat Mishra
    • June 11, 2020 20:57
    0 votes 2 comments
  • Picard RnaSeqMetrics CORRECT_STRAND_READS and INCORRECT_STRAND_READS
    • runxuan
    • June 05, 2020 15:16
    0 votes 1 comment
  • How to find or generate common germline variant sites VCF required by GetPileupSummaries
    • Antti Koskenalho
    • May 27, 2020 06:22
    1 vote 4 comments
  • How is tumor_f in Funcotator MAF Answered
    • Robert Bremel
    • May 26, 2020 17:11
    0 votes 3 comments
  • CollectAllelicCounts interval_list Answered
    • jejacobs23
    • May 18, 2020 22:33
    1 vote 15 comments
  • mutect2 multi-sample Answered
    • zhao shilin
    • May 07, 2020 17:27
    • Edited
    0 votes 29 comments
  • GenomAD files for MuTect2 Answered
    • Felix
    • May 06, 2020 10:18
    0 votes 9 comments
  • GATK4 Best Practices -- SetNmMdAndUqTags
    • Alijah O'Connor
    • April 28, 2020 23:37
    0 votes 1 comment
  • ask for target sequencing pipeline code using Mutect2 (gatk 4.1.7.0)
    • Zhi Zhang
    • April 27, 2020 14:43
    0 votes 1 comment
  • ASEReadCounter and overlapping paired reads
    • Björn Gylemo
    • April 21, 2020 09:07
    0 votes 1 comment
  • BQSR --use-original-qualities
    • Alijah O'Connor
    • April 20, 2020 22:02
    • Edited
    0 votes 1 comment
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