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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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  • Calling somatic CNVs Answered
    • Yasin Uzun
    • September 09, 2020 02:34
    0 votes 6 comments
  • GenotypeGVCFs only accepts single combinedGVCF? CombineGVCFs & genomicsdb errors... .interval_list subset Answered
    • Mingzhou Fu
    • July 29, 2021 22:42
    0 votes 12 comments
  • Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores? Answered
    • Rodrigo Cabrera
    • July 29, 2021 20:00
    0 votes 1 comment
  • Known Sites for BQSR Answered
    • T. Li
    • December 07, 2020 22:26
    5 votes 5 comments
  • CollectAllelicCounts interval_list Answered
    • jejacobs23
    • May 18, 2020 22:33
    1 vote 15 comments
  • Truth set download page for BQSR Answered
    • prasundutta87
    • January 29, 2021 11:54
    0 votes 2 comments
  • RADseq/MIGseq denovo SNP calling in tetraploid plants Answered
    • Alfons Weig (ARW)
    • December 04, 2020 13:02
    • Edited
    0 votes 3 comments
  • Does CollectReadCounts Count Fragments or Individual Reads? Answered
    • Fong Chun Chan
    • July 16, 2021 09:19
    • Edited
    0 votes 3 comments
  • every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered
    • 이한새
    • July 21, 2021 00:49
    • Edited
    0 votes 4 comments
  • MarkDuplicates not checking sequences Answered
    • Naomie Abecassis
    • July 13, 2021 13:35
    0 votes 3 comments
  • Best practice to deal with spanning deletion for downstream analysis Answered
    • Degang Wu
    • November 05, 2020 03:03
    0 votes 3 comments
  • Using -"-allow-old-rms-mapping-quality-annotation-data" to force genotyping gvcf created with old version Answered
    • Muriel Gros-Balthazard
    • June 25, 2021 08:54
    0 votes 1 comment
  • GATK VariantEval no concordance between dbSNP and our data Answered
    • Pierre_Bioinfo
    • May 03, 2021 07:50
    0 votes 6 comments
  • Theorical model for Active region detection Answered
    • Naomie Abecassis
    • June 22, 2021 14:26
    0 votes 6 comments
  • BQSR --use-original-qualities
    • Alijah O'Connor
    • April 20, 2020 22:02
    • Edited
    0 votes 1 comment
  • ASEReadCounter and overlapping paired reads
    • Björn Gylemo
    • April 21, 2020 09:07
    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
  • GATK4 Best Practices -- SetNmMdAndUqTags
    • Alijah O'Connor
    • April 28, 2020 23:37
    0 votes 1 comment
  • What are the initial files required in order to go through the Data Preprocessing, Variant Discovery and IGV phases of Genomic analysis? Answered
    • Kountay Dwivedi
    • October 21, 2020 15:52
    0 votes 3 comments
  • Difference between GATK Germline CNV Pipeline vs Genome STRiP? Answered
    • Muhammad Shoaib Akhtar
    • October 29, 2020 08:49
    0 votes 8 comments
  • error-handling-end-exit-codes-in-gatk
    • Kshama Aswath
    • August 19, 2020 18:50
    0 votes 1 comment
  • GenomAD files for MuTect2 Answered
    • Felix
    • May 06, 2020 10:18
    0 votes 9 comments
  • ASEReadCounter count each read only once or not
    • Qingnan Liang
    • September 02, 2020 00:38
    0 votes 1 comment
  • Germline CNV vs HaplotypeCaller/indels
    • Heba B abusamra
    • September 03, 2020 06:02
    0 votes 1 comment
  • What is the correct step? VQSR and CNNScoreVariants? Answered
    • Damian Fermin
    • September 04, 2020 17:29
    0 votes 2 comments
  • BQSR Spark: Why Beta? Answered
    • Tavi Nathanson
    • September 18, 2020 22:51
    0 votes 3 comments
  • After SNPs and INDELs are extracted, can they be recombined later? Answered
    • Daniel Westcott
    • July 23, 2020 23:09
    0 votes 1 comment
  • Mulitple mapped reads in germline CNV caller (GermlineCNVCaller) Answered
    • chrl
    • July 29, 2020 07:50
    0 votes 1 comment
  • The base of logarithm for VQSLOD
    • Edward David
    • August 04, 2020 21:36
    0 votes 1 comment
  • Funcotator misses many Cosmic fields - update possible?
    • Tjitske de Vries
    • August 13, 2020 08:41
    0 votes 1 comment
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