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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 recent activity Newest post Recent activity Votes Comments
  • Workflow for WES/WGS
    • Sheryl
    • September 15, 2023 01:27
    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
  • ReorderSam: New reference sequence does not contain a matching contig for ERCC-00002
    • Cora Olpe
    • October 03, 2023 08:25
    0 votes 1 comment
  • Struggling to assign read groups with AddOrReplaceReadgroups
    • Cora Olpe
    • October 01, 2023 15:29
    0 votes 2 comments
  • Issue with Running MuTect in GATK Version Compatibility
    • 김수영
    • August 31, 2023 06:44
    0 votes 3 comments
  • GATK MarkDuplicates Missing output file
    • Gilgamesh
    • August 30, 2023 17:35
    1 vote 5 comments
  • Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered
    • Elisabetta Manduchi
    • April 12, 2022 15:00
    0 votes 5 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
  • Call input and runtime attributes evaluation failed for PairedFastQsToUnmappedBAM
    • Ananya Saji
    • April 21, 2023 06:29
    0 votes 1 comment
  • CollectInsertSizeMetrics can't find R
    • Craig Amundsen
    • July 21, 2023 22:15
    0 votes 6 comments
  • STAR and GATK RNAseq based SNP detection
    • Jahn Davik
    • May 03, 2023 08:14
    0 votes 1 comment
  • VCF file SNP ID missing
    • Wondessen Ayalew
    • June 29, 2023 08:48
    • Edited
    0 votes 9 comments
  • PICARD/Gradle build fail
    • Olivia Cheng
    • June 28, 2023 22:52
    0 votes 3 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
  • BaitDesigner Fasta Output Missing Gene Names
    • Tapoka M
    • April 12, 2023 10:27
    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
  • Steps For GATK-gCNV pipleline on Exome Data
    • Y R
    • April 03, 2023 15:30
    • Edited
    0 votes 12 comments
  • HaplotypeCaller produces VCF's from 1KG data that have low SNP overlap
    • Nils Paffen
    • April 11, 2023 09:00
    • Edited
    0 votes 1 comment
  • Mutect2 PON
    • Sheryl
    • April 17, 2023 04:28
    0 votes 1 comment
  • ApplyBQSR
    • Wondessen Ayalew
    • February 23, 2023 06:19
    0 votes 10 comments
  • Running GenomicsDBImport/CombineGVCFs on Azure leads to User Error: Illegal argument value
    • Martin Danner
    • April 18, 2023 10:29
    • Edited
    0 votes 1 comment
  • Interval list and the “Mate not found” error in WES data
    • LY Wang
    • April 07, 2023 13:19
    0 votes 2 comments
  • Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"
    • Anna Gatseva
    • March 22, 2023 11:00
    0 votes 1 comment
  • somatic CNV PoN
    • Sheryl
    • March 06, 2023 20:00
    • Edited
    0 votes 1 comment
  • Mutect2 wdl interval list and scatter count
    • Sheryl
    • March 06, 2023 02:19
    • Edited
    0 votes 3 comments
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