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. Somatic

Somatic

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
  • LeftAlignIndels issue - process done in 5 seconds and output file is only 3kb
    • Jonas Andersson
    • December 07, 2020 19:02
    • Edited
    0 votes 3 comments
  • Missing mutations
    • vctrymao
    • December 03, 2020 20:41
    0 votes 7 comments
  • strand bias and orientation bias
    • that girl
    • December 02, 2020 06:51
    4 votes 1 comment
  • DepthOfCoverage intervals
    • Andrea Franceschini
    • December 01, 2020 12:35
    0 votes 1 comment
  • how to see 2 or more variants are in the same read
    • that girl
    • November 28, 2020 09:29
    0 votes 1 comment
  • Funcotator Errors : I/O error in the advisory file locking logic (disk I/O error)
    • Min-Hwan Sohn
    • November 26, 2020 03:56
    • Edited
    1 vote 1 comment
  • CalculateContamination: Multiple KernelSegmenter warnings
    • ISmolicz
    • November 23, 2020 15:29
    0 votes 17 comments
  • GenomicsDBImport: are all intervals being processed or is there an error? Answered
    • ISmolicz
    • November 21, 2020 17:55
    0 votes 4 comments
  • Mutect2 panel of normals and germline source files with incompatible contigs
    • Field -Ye Tian
    • November 18, 2020 06:11
    0 votes 5 comments
  • How do I get known-SNP, Indel files in hg19 version?
    • Ashi
    • November 16, 2020 19:48
    0 votes 2 comments
  • bwa index doesn't create .alt file in hg38 Answered
    • MatZ
    • November 12, 2020 14:15
    1 vote 8 comments
  • FilterMutectCalls
    • Nejla Ozirmak Lermi
    • November 11, 2020 15:48
    0 votes 5 comments
  • Which gnomAD version is used for somatic-hg38_af-only-gnomad.hg38.vcf.gz
    • Antti Koskenalho
    • November 05, 2020 09:21
    0 votes 2 comments
  • Running Mutect wdl on Cromwell
    • Milena Stanojevic
    • November 04, 2020 13:15
    0 votes 3 comments
  • How do I merge f1r2.tar.gz files when parallelizing Mutect2 pipeline?
    • Jenifer
    • October 28, 2020 17:25
    • Edited
    1 vote 1 comment
  • Mutect2 clustered_events filtered
    • hansonl
    • October 28, 2020 03:49
    0 votes 1 comment
  • VariantAnnotator only reports coverage and other info when there are reads on the ALT allele
    • Wout Megchelenbrink
    • October 23, 2020 19:11
    0 votes 1 comment
  • Using CollectOxoGMetrics to determine biological 8oxoG
    • Danielle Reid
    • October 21, 2020 15:38
    0 votes 1 comment
  • VariantAnnotator returns NullPointerException
    • Wout Megchelenbrink
    • October 21, 2020 12:29
    0 votes 6 comments
  • Germline false positives in Mutect2
    • TMB
    • October 21, 2020 02:37
    0 votes 9 comments
  • Error in FilterMutectCalls
    • Enrique Vázquez de Luis
    • October 20, 2020 22:18
    0 votes 4 comments
  • Memory error with Mutect2
    • Kimberly McLaughlin
    • October 20, 2020 19:57
    0 votes 1 comment
  • Error while running CreateReadCountPanelOfNormals
    • bdong
    • October 18, 2020 08:50
    0 votes 1 comment
  • MarkDuplicatesSpark error missing Read Group fields
    • Field -Ye Tian
    • October 09, 2020 16:45
    1 vote 1 comment
  • Missed Somatic CNV call with significant log2 values
    • Ashini Bolia
    • October 07, 2020 19:01
    0 votes 9 comments
  • MuTect2: There are too many keys for the sample
    • nilshomer
    • October 06, 2020 18:52
    0 votes 3 comments
  • How do I get MuTect2 to output the contig lines in the VCF header?
    • nilshomer
    • October 06, 2020 18:39
    0 votes 2 comments
  • Missing contig lines in thh Somatic b37 gnomad sites-only VCF header
    • nilshomer
    • October 06, 2020 18:21
    0 votes 2 comments
  • A USER ERROR has occurred: Bad input: Sample R-HT77.merged.sorted.bam is not in BAM header: [R-HT72, R-HT72-P2, R-HT72-at-diagnosis-FFPE, R-HT72-p0, R-HT72-p1, R-HT77, R-HT77-P3, R-HT77-P3-Cell-line, R-HT77-p0, R-HT77-p1, R-HT77-p2]
    • Asha
    • October 03, 2020 01:35
    • Edited
    0 votes 7 comments
  • A USER ERROR has occurred: af-only-gnomad.hg38.vcf.gz because no suitable codecs found Answered
    • Asha
    • October 02, 2020 18:08
    0 votes 9 comments
  • «
  • ‹
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
  • 8
  • 9
  • 10
  • ›
  • »

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You 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