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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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  • gatk FilterByOrientationBias Answered
    • Nishtha Tanwar
    • May 04, 2021 09:15
    0 votes 2 comments
  • GenomicsDBImport java error
    • TONG ZHOU TAO
    • May 04, 2021 06:33
    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
  • What does mutect2 do if two bams are input and --normal-sample is not specified? Answered
    • Tyler Borrman
    • April 27, 2021 05:07
    • Edited
    0 votes 1 comment
  • ApplyBQSRSpark ApplyBQSR has different results
    • AMN
    • April 22, 2021 15:40
    • Edited
    0 votes 3 comments
  • GC DROPOUT AND AT DROPOUT Answered
    • asqt96
    • April 22, 2021 13:16
    0 votes 1 comment
  • Determining Optimal Number of Samples to include in Panel of Normal Answered
    • Gannon Cottone
    • April 16, 2021 16:56
    0 votes 2 comments
  • every exon junctions in Bam files got softclipped after run SplitNCigarReads Answered
    • 이한새
    • July 21, 2021 00:49
    • Edited
    0 votes 4 comments
  • How does Picard basecalling make decisions on NovaSeq data? Answered
    • James Webber
    • April 14, 2021 17:12
    0 votes 4 comments
  • If base quality scores set at 2 for clipped regions are restored to the original score with MergeBamAlignment, how will clipped regions not contribute to downstream analyses? Planned
    • ISmolicz
    • April 07, 2021 15:07
    • Edited
    0 votes 0 comments
  • How do adapter sequences not contribute to alignment if the base quality is set to 2 with SamToFastq but BWA-MEM does not consider base quality scores? Answered
    • ISmolicz
    • April 07, 2021 14:37
    • Edited
    0 votes 5 comments
  • GATK 4.2.0.0 Haplotype caller --genotyping_mode DISCOVERY Option Answered
    • M.R-E.H
    • April 07, 2021 11:30
    0 votes 2 comments
  • Error remove 0x1 from alternate contigs tutorial Answered
    • Linda Do
    • April 05, 2021 16:18
    0 votes 5 comments
  • CreateSomaticPanelOfNormals BETA tag Answered
    • G E
    • April 01, 2021 19:38
    0 votes 2 comments
  • Sensitivity analysis for GATK CNV PoN Answered
    • Kimal Rajapakshe
    • March 29, 2021 21:51
    0 votes 1 comment
  • Mutect2 merge stats Answered
    • Saskia
    • March 29, 2021 15:05
    0 votes 2 comments
  • Error HaplotypeCaller from alternate contigs tutorial Answered
    • Linda Do
    • March 25, 2021 20:08
    0 votes 4 comments
  • BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used? Answered
    • ISmolicz
    • March 24, 2021 18:27
    • Edited
    0 votes 4 comments
  • Germline sites in Mutect2 Answered
    • G E
    • March 19, 2021 04:39
    • Edited
    0 votes 11 comments
  • Potential updates to GATK HaplotypeCaller documentation
    • Amit
    • March 17, 2021 17:00
    • Edited
    0 votes 1 comment
  • Alt Contig tutorial question Answered
    • Linda Do
    • March 15, 2021 05:22
    0 votes 7 comments
  • Three questions about calling CNV in Germline. Answered
    • rq m
    • March 12, 2021 03:23
    • Edited
    0 votes 7 comments
  • Mutect2 panel of normals design Answered
    • Jagadheshwar Balan
    • March 08, 2021 14:45
    0 votes 2 comments
  • Truth set download page for BQSR Answered
    • prasundutta87
    • January 29, 2021 11:54
    0 votes 2 comments
  • Converting Reference Genomes from b37 to hg19
    • Abhi Agarwal
    • December 30, 2020 19:12
    0 votes 4 comments
  • Known Sites for BQSR Answered
    • T. Li
    • December 07, 2020 22:26
    5 votes 5 comments
  • RADseq/MIGseq denovo SNP calling in tetraploid plants Answered
    • Alfons Weig (ARW)
    • December 04, 2020 13:02
    • Edited
    0 votes 3 comments
  • HaplotypeCaller vcf file analysis Answered
    • ziliang
    • November 23, 2020 14:18
    0 votes 2 comments
  • Unix pipe support and SAM fields used in Variant Calling pipeline Answered
    • Rocco Gabriele Storace
    • November 19, 2020 13:38
    0 votes 2 comments
  • How can I get AF for each sample in GVC JointGenotyping mode? Answered
    • Jenifer
    • November 19, 2020 08:25
    0 votes 3 comments
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