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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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New User Advice

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Show all All Planned Not planned Completed Answered No status Sort by votes Newest post Recent activity Votes Comments
  • Splitting a final filtered VCF file based on sample list and MAF Impact
    • Conor Sexton
    • November 23, 2023 12:47
    1 vote 2 comments
  • GATK MarkDuplicates Missing output file
    • Gilgamesh
    • August 30, 2023 17:35
    1 vote 5 comments
  • Scatter Gather principle by chromosome on Gatk
    • Sushant Sawant
    • November 28, 2022 06:44
    • Edited
    1 vote 2 comments
  • Proper way to prepare .bam for MarkDuplicatesSpark Answered
    • samuel
    • July 06, 2022 06:46
    1 vote 3 comments
  • Running best practices workflow step-by-step in command line
    • limetree
    • June 04, 2021 05:12
    1 vote 5 comments
  • A fatal error was detected by the Java Runtime Environment when running HaplotypeCaller
    • Kaina Millan
    • November 30, 2023 17:36
    0 votes 2 comments
  • VariantFiltration filtering all SNPs for all samples to missing
    • Wiebe Kooistra
    • November 30, 2023 16:04
    0 votes 0 comments
  • JexlEngine - ![0,14]: 'ReadPosRankSum < -20.0;' undefined variable ReadPosRankSum For GATK VariantFiltration
    • Y R
    • November 19, 2023 15:31
    • Edited
    0 votes 8 comments
  • Required arguement in MergeBamAlignment
    • Shvartsman
    • November 16, 2023 06:46
    0 votes 1 comment
  • Asking for Guidance on Variant Calling Pipeline - Biological replicates
    • H.T
    • November 14, 2023 14:07
    • Edited
    0 votes 1 comment
  • CombineGVCFs or GenomicDBImport for consolidating haploid bacterial GVCFs
    • Conor Sexton
    • November 09, 2023 13:30
    0 votes 2 comments
  • Whole Genome pipe for use with non whole genome data
    • Liam McIntyre
    • October 27, 2023 03:30
    0 votes 3 comments
  • Splitting .g.vcf file by chromosome.
    • Nikee Shrestha
    • October 18, 2023 01:46
    0 votes 1 comment
  • ReorderSam: New reference sequence does not contain a matching contig for ERCC-00002
    • Cora Olpe
    • October 03, 2023 08:25
    0 votes 1 comment
  • SplitNCigarReads: Contig ERCC-ERCC-00002 given as location, but this contig isn't present in the Fasta sequence dictionary
    • Cora Olpe
    • October 02, 2023 13:09
    0 votes 2 comments
  • Struggling to assign read groups with AddOrReplaceReadgroups
    • Cora Olpe
    • October 01, 2023 15:29
    0 votes 2 comments
  • Workflow for WES/WGS
    • Sheryl
    • September 15, 2023 01:27
    0 votes 1 comment
  • Issue with Running MuTect in GATK Version Compatibility
    • 김수영
    • August 31, 2023 06:44
    0 votes 3 comments
  • cnv_germline_case_workflow.wdl
    • Sheryl
    • August 23, 2023 05:10
    0 votes 3 comments
  • GATK-SV HPC VM hardware requirements
    • Georgia Hosking
    • August 14, 2023 07:18
    • Edited
    0 votes 1 comment
  • CollectInsertSizeMetrics can't find R
    • Craig Amundsen
    • July 21, 2023 22:15
    0 votes 6 comments
  • PICARD/Gradle build fail
    • Olivia Cheng
    • June 28, 2023 22:52
    0 votes 3 comments
  • VCF file SNP ID missing
    • Wondessen Ayalew
    • June 29, 2023 08:48
    • Edited
    0 votes 9 comments
  • Mitochondrial pipeline requirement
    • Sheryl
    • June 15, 2023 01:55
    0 votes 1 comment
  • ExomeSingleSample wdl
    • Sheryl
    • June 08, 2023 02:07
    0 votes 1 comment
  • get the basics for Haplotypecaller
    • Maarten Nijenhuis
    • June 02, 2023 10:37
    0 votes 2 comments
  • STAR and GATK RNAseq based SNP detection
    • Jahn Davik
    • May 03, 2023 08:14
    0 votes 1 comment
  • Best practice with read groups
    • Sheryl
    • April 27, 2023 00:43
    0 votes 1 comment
  • Download GATK4 required packages in docker container
    • Marcela Martinez
    • April 25, 2023 22:29
    0 votes 1 comment
  • Is It Allowed To Submit An Entire Code For Review?
    • Y R
    • April 23, 2023 10:09
    0 votes 2 comments
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