Logo
User Guide Tool Index Blog Forum DRAGEN-GATK Events Download GATK4
Sign in

Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

  1. GATK
  2. Community
  3. Other

Other

Follow New posts New posts and comments

Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • Any recommended criteria for filtering Mixed and MNP variants with VariantFiltration
    • Phongphak Khongthon
    • July 06, 2020 12:48
    0 votes 1 comment
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    0 votes 10 comments
  • Extract individual samples from combined gvcf file
    • Balat
    • July 03, 2020 01:20
    0 votes 1 comment
  • Inquiry about the GATK Best Practices for variant calling on RNAseq
    • Benjamin Hing
    • July 02, 2020 00:24
    0 votes 1 comment
  • gatk3-register
    • touyupang
    • July 01, 2020 05:23
    0 votes 1 comment
  • How to reduce the processing time of BwaMemIndexImageCreator
    • Ganesh P Kumar
    • June 25, 2020 07:10
    0 votes 2 comments
  • SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals
    • Linda Do
    • June 22, 2020 21:46
    0 votes 3 comments
  • Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
    • Argonaut44
    • June 23, 2020 18:09
    • Edited
    0 votes 3 comments
  • evaluation of the VCF file which is made using GATK
    • behzad
    • June 22, 2020 11:41
    0 votes 1 comment
  • Funcotator: Sift and Polyphen fields are empty in MAF output
    • PS
    • June 19, 2020 21:53
    0 votes 1 comment
  • resource bundle b37
    • hirokomatsui
    • June 19, 2020 00:20
    0 votes 1 comment
  • MarkDuplicatesSparks not removing some duplicates?
    • Tom Morrison
    • June 18, 2020 14:55
    0 votes 15 comments
  • copyright issue
    • Özlem Okutman
    • June 16, 2020 13:17
    0 votes 2 comments
  • Failed variants in BQSR and VQSR training sets
    • tnsanger
    • June 18, 2020 14:51
    • Edited
    0 votes 3 comments
  • Output of PossibleDeNovo
    • Sanat Mishra
    • June 11, 2020 20:57
    0 votes 1 comment
  • Genomestrip cannot find --ploidyMapFile
    • Swanthana Rekulapally
    • June 11, 2020 20:23
    0 votes 9 comments
  • IlluminaBasecallsToSam - barcode was not expected
    • Vincent Hahaut
    • June 10, 2020 19:04
    0 votes 1 comment
  • When will AnalyzeCovariates support R/4.0
    • Qi Yu
    • June 09, 2020 21:20
    0 votes 1 comment
  • Error when running FastaAlternateReferenceMaker
    • Fritz Forbang
    • June 09, 2020 10:27
    0 votes 1 comment
  • GenomicsDBImport does not recognize option --genomicsdb-update-workspace-path
    • Jose Luis Gualdron
    • June 08, 2020 08:08
    0 votes 2 comments
  • humanG1Kv37 to hg38 liftover issues
    • brian miller
    • June 06, 2020 00:44
    • Edited
    0 votes 3 comments
  • Error in running CollectGcBiasMetrics
    • SrivastavaS
    • June 05, 2020 17:30
    0 votes 1 comment
  • Picard RnaSeqMetrics CORRECT_STRAND_READS and INCORRECT_STRAND_READS
    • runxuan
    • June 05, 2020 15:16
    0 votes 1 comment
  • Combining SE and PE reads for SNP calling
    • Cameron Johnson
    • June 04, 2020 15:04
    0 votes 1 comment
  • ReciprocalOverlapAnnotator error for Illumina data (both ERDS and CNVnator)
    • Ghausia Begum
    • June 04, 2020 04:22
    0 votes 5 comments
  • Mutect2: mitochondria mode weird
    • Roberto Sirica
    • June 03, 2020 14:46
    0 votes 2 comments
  • SelectVariants v4.1.6.0 doesn't select the variants as expected
    • ABours
    • June 02, 2020 13:26
    0 votes 5 comments
  • VariantRecalibrator throwing VariantRecalibratorEngine - Evaluate datum returned a NaN warning then crashing with empty tranches file.
    • David Murphy
    • June 02, 2020 12:58
    • Edited
    0 votes 2 comments
  • something wrong with MarkDuplicatesSpark
    • charles_cai
    • June 02, 2020 10:09
    0 votes 1 comment
  • GenotypeGVCF Output Only 1 Locus
    • Himawari
    • June 01, 2020 11:47
    • Edited
    0 votes 1 comment
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • 8
  • 9
  • 10
  • ›
  • »

Welcome

GATK Announcements

Read Before You Post

How to Write a Post

Get Email Notifications

Didn't find what you were looking for?

New post

Quick Links

GATK Latest Releases

Known Issues & Troubleshooting

Submitting a Bug Report

How to Track a Github issue

GATK on the Cloud with Terra

Recent GATK News

GATK Blog Posts

GATK Twitter Page

About the GATK community

  • 133,119 Total Users
  • 0 Comments
  • 0 Posts
  • 0 Votes

footer-logo © Broad Institute

  • twitter icon
  • facebook icon
  • linkedin icon
Powered by Zendesk