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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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  • Single sample germline - VQSR+CNN or just CNN
    • Jordan Russell
    • March 18, 2022 15:45
    0 votes 5 comments
  • JEXL expression for filtering on AD (SelectVariants / FastaAlternateReferenceMaker)
    • Yanis Chrys
    • August 19, 2021 11:35
    0 votes 4 comments
  • Converting Reference Genomes from b37 to hg19
    • Abhi Agarwal
    • December 30, 2020 19:12
    0 votes 4 comments
  • Questions Regarding VCF Files Found in hg38 Public Resource Bundle
    • Sara Coder
    • June 17, 2020 23:18
    0 votes 4 comments
  • How to find or generate common germline variant sites VCF required by GetPileupSummaries
    • Antti Koskenalho
    • May 27, 2020 06:22
    1 vote 4 comments
  • Confirmation that Mutect2 /haplotype caller only use reads mapped within the active region
    • JW
    • June 03, 2021 16:19
    1 vote 3 comments
  • ApplyBQSRSpark ApplyBQSR has different results
    • AMN
    • April 22, 2021 15:40
    • Edited
    0 votes 3 comments
  • What do the two different minimum base quality filters do in Mutect2?
    • Nick Bernstein
    • August 14, 2020 21:25
    0 votes 3 comments
  • Map reads to a reference with alternate contigs like GRCH38 using GATK4
    • neethukrishna Kausthubham
    • July 29, 2020 10:14
    0 votes 3 comments
  • How does Genomicsdbimport for polyploids work?
    • Homa Papoli
    • October 25, 2021 08:57
    0 votes 2 comments
  • Mark duplicates in merged bam files sorted by coordinates
    • Priyadarshini Thirunavukkarasu
    • September 14, 2021 08:16
    0 votes 2 comments
  • What does PCT_MIX from CreateVerifyIDIntensityContaminationMetricsFile mean?
    • Lucas Taniguti
    • June 21, 2021 13:40
    0 votes 2 comments
  • 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
  • Limit core use of DetermineGermlineContigPloidy & GermlineCNVCaller
    • Blaz Vrhovsek
    • June 30, 2022 11:27
    1 vote 1 comment
  • HaplotypeCaller using one sample split in two bam files
    • elena vigorito
    • June 28, 2022 09:16
    0 votes 1 comment
  • germline mutation calling using per-sample module
    • chenglei
    • June 08, 2022 16:06
    0 votes 1 comment
  • Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
    • tahi
    • February 22, 2022 08:48
    0 votes 1 comment
  • What's wrong with my GATK HaplotypeCaller step's codes?
    • Han Li
    • November 29, 2021 05:18
    0 votes 1 comment
  • Unable to find full Best Practices workflow for short variant joint genotyping
    • Kirsten Dimmler
    • November 23, 2021 17:41
    0 votes 1 comment
  • How can I get Sample Summary
    • rq m
    • November 19, 2021 08:10
    • Edited
    0 votes 1 comment
  • GATK4.2.3.0 HaplotypeCaller error
    • Alicia
    • November 13, 2021 12:49
    0 votes 1 comment
  • Difference between the different annotation groups available in GATK
    • Shashank Nagaraja
    • October 04, 2021 22:15
    2 votes 1 comment
  • GenomicsDBImport java error
    • TONG ZHOU TAO
    • May 04, 2021 06:33
    0 votes 1 comment
  • Potential updates to GATK HaplotypeCaller documentation
    • Amit
    • March 17, 2021 17:00
    • Edited
    0 votes 1 comment
  • 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
  • Funcotator misses many Cosmic fields - update possible?
    • Tjitske de Vries
    • August 13, 2020 08:41
    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
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