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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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Show all All Planned Not planned Completed Answered No status Sort by comments Newest post Recent activity Votes Comments
  • Mutect2 Funcotator error
    • MPetlj
    • June 08, 2020 16:15
    0 votes 31 comments
  • Mutect2-PON Storage object issue when running across multiple samples?
    • MPetlj
    • June 22, 2020 15:57
    0 votes 30 comments
  • java.lang.OutofMemoryError: GC overhead limit exceeded Answered
    • Jack Prazich
    • May 03, 2021 16:54
    0 votes 28 comments
  • Funcotator errors
    • MPetlj
    • August 05, 2020 23:40
    0 votes 27 comments
  • Mutect2 issue with --force-active: not all regions are active Answered
    • Maria Litovchenko
    • September 08, 2021 17:29
    1 vote 25 comments
  • Artefactual calls using Mutect2 on RNAseq data Answered
    • cmartinezruiz
    • February 14, 2020 10:46
    0 votes 25 comments
  • The depth of SNV/InDels calculated by Mutect2 in GATK4.2.0.0 is much lower than real sequencing depth, why? Answered
    • Ce Wang
    • May 25, 2021 06:08
    • Edited
    0 votes 19 comments
  • Empty final PON vcf file from 7 samples Answered
    • Yun Yu
    • January 04, 2021 08:42
    0 votes 18 comments
  • Mutect2 PON - gnomAD input?
    • MPetlj
    • June 03, 2020 14:36
    0 votes 18 comments
  • CalculateContamination: Multiple KernelSegmenter warnings
    • ISmolicz
    • November 23, 2020 15:29
    0 votes 17 comments
  • Mutect2 doesn't produce stats file
    • Serena Ferraresso
    • June 16, 2020 09:46
    0 votes 17 comments
  • Broad hg38 ICE interval list Answered
    • Chet Birger
    • February 20, 2020 19:16
    3 votes 17 comments
  • Error while running ModelSegments Answered
    • onurerdoganmd
    • November 09, 2021 20:52
    0 votes 15 comments
  • Mutect2 PoN - GenomicsDBImport creates empty DB Answered
    • Enrico Cocchi
    • July 14, 2021 10:37
    • Edited
    0 votes 15 comments
  • Increased number of false positives in Mutect2 GATK 4.1.7.0
    • registered_user
    • May 18, 2020 12:53
    • Edited
    0 votes 15 comments
  • Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations
    • Saba
    • April 29, 2020 15:54
    • Edited
    1 vote 15 comments
  • In Mutect2 force-calling allele via --alleles does not force-call the allele Answered
    • Rahul Gupta
    • February 04, 2022 17:13
    • Edited
    0 votes 14 comments
  • Mutect2 - somatic variant calling with/without matched normal sample
    • D B
    • February 26, 2020 19:33
    • 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
  • GGA-mode gives PASS tag while the site failed in the normal workflow
    • xiucz
    • November 16, 2021 03:22
    • Edited
    0 votes 13 comments
  • Funcotator data source not correct Answered
    • Jamie Xie
    • March 29, 2021 20:42
    • Edited
    0 votes 13 comments
  • Mutect2 multi-sample pipeline
    • manolis
    • July 20, 2020 14:04
    0 votes 13 comments
  • Option "--dont-use-soft-clipped-bases" does not seem to work in Mutect2
    • janrehker
    • June 02, 2020 13:25
    • Edited
    0 votes 13 comments
  • Picard Liftover hg38 to hg19 Error. Answered
    • Wu, Tsung-Jung
    • March 31, 2020 10:18
    • Edited
    0 votes 13 comments
  • Mutect2 - Need one or two reads to construct a fragment
    • D B
    • January 17, 2020 14:43
    0 votes 13 comments
  • Why do I get 'java.lang.IllegalArgumentException: Dictionary cannot have size zero' when using GetPileupSummaries? Answered
    • Ruiqiao Bai
    • September 12, 2021 01:06
    0 votes 12 comments
  • CollectAllelicCounts- Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded Answered
    • rahelp
    • May 16, 2021 13:17
    0 votes 12 comments
  • Why do a clear expected variant not show up in the Mutect2 vcf file Answered
    • Nabeel Ahmed
    • April 07, 2021 09:13
    0 votes 12 comments
  • Issues with Java heap space in CollectAllelicCounts
    • jejacobs23
    • August 18, 2020 22:52
    0 votes 12 comments
  • GenomicsDBImport error: USER ERROR has occurred: Duplicate sample: 1. Sample was found in both file: Completed
    • Yuna Son
    • August 08, 2020 02:58
    0 votes 12 comments
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