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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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Somatic

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Show all All Planned Not planned Completed Answered No status Sort by votes Newest post Recent activity Votes Comments
  • strand bias and orientation bias
    • that girl
    • December 02, 2020 06:51
    5 votes 2 comments
  • Broad hg38 ICE interval list Answered
    • Chet Birger
    • February 20, 2020 19:16
    3 votes 17 comments
  • Custom made Panel of Normals required?
    • Pedro Miguel Raposo
    • July 07, 2020 10:01
    • Edited
    2 votes 2 comments
  • Generating ACS like output from new GATK CNV pipeline (WGS)
    • Jett Crowdis
    • June 26, 2020 18:11
    2 votes 4 comments
  • SOLVED: Get read counts of Mutect2 somatic variants
    • Mariana E. M.
    • August 11, 2023 15:17
    • Edited
    1 vote 1 comment
  • Mutect2 - No .stats file created with SLURM
    • Ryan Yordanoff
    • June 20, 2023 23:11
    1 vote 2 comments
  • GATK Muteck2 missing call Answered
    • Marco Chiapello
    • September 23, 2022 09:14
    1 vote 2 comments
  • Funcotator maf has different alt allele than vcf for some variants
    • Balthasar
    • July 11, 2022 11:34
    1 vote 1 comment
  • Creating Panel of Normals (PoN) from Blood Sample of cancer patients Answered
    • Ranjan J. Sarma
    • July 05, 2022 08:15
    • Edited
    1 vote 14 comments
  • Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start Answered
    • yqiu
    • January 06, 2022 00:13
    • Edited
    1 vote 13 comments
  • empty pon vcf file Answered
    • Lait
    • November 03, 2021 14:32
    1 vote 1 comment
  • Mutect2 calls long deletion with absolutely zero read support Answered
    • Brian Wiley
    • October 19, 2021 00:53
    1 vote 3 comments
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Broad hg19 TWIST interval list Answered
    • Tejas Jammihal
    • January 20, 2021 17:14
    1 vote 4 comments
  • 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
  • bwa index doesn't create .alt file in hg38 Answered
    • MatZ
    • November 12, 2020 14:15
    1 vote 8 comments
  • How do I merge f1r2.tar.gz files when parallelizing Mutect2 pipeline?
    • Jenifer
    • October 28, 2020 17:25
    • Edited
    1 vote 1 comment
  • MarkDuplicatesSpark error missing Read Group fields
    • Field -Ye Tian
    • October 09, 2020 16:45
    1 vote 1 comment
  • CalculateContamination "there is no such column: contig"
    • Jensen Richardson
    • July 05, 2020 18:02
    1 vote 8 comments
  • gatk CollectAllelicCounts error
    • peterchung
    • May 26, 2020 03:23
    • Edited
    1 vote 6 comments
  • Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations
    • Saba
    • April 29, 2020 15:54
    • Edited
    1 vote 15 comments
  • Mutect2 - somatic variant calling with/without matched normal sample
    • D B
    • February 26, 2020 19:33
    • Edited
    1 vote 14 comments
  • MergeBamAlignment Error: ArrayIndexOutOfBoundsException
    • Jared Jurss
    • February 19, 2020 22:02
    1 vote 3 comments
  • Problems combining gVCFs that have thousands of scaffolds
    • Dch
    • February 11, 2020 23:24
    • Edited
    1 vote 5 comments
  • Mutect2 variant calling output with tumor and matched normal: 0/1 in all variants called
    • RicPin
    • February 10, 2020 15:41
    • Edited
    1 vote 5 comments
  • Call germline mutations from Mutect2
    • Chadi Saad
    • January 14, 2020 10:30
    1 vote 3 comments
  • Mutect w/ panel of normal throwing errors, even though mutect w/o panel of normal works fine.
    • Eduardo Maury
    • September 09, 2023 18:45
    0 votes 1 comment
  • Details about the filters used in a previous version of FilterMutectCalls
    • Tal Gutman
    • September 04, 2023 08:13
    0 votes 7 comments
  • Mutect2 overlapping reads behavior with --pcr-snv-qual parameter
    • Semen Leyn
    • September 03, 2023 05:15
    0 votes 2 comments
  • Mutect2 in multisample mode slows at HLA Loci in hg38 alt-aware alignments
    • Nathaniel Alzofon
    • August 29, 2023 04:44
    • Edited
    0 votes 1 comment
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