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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 newest post Newest post Recent activity Votes Comments
  • Mutect2 LearnReadOrientationModel Memory Error
    • Arvind Ravi
    • September 29, 2020 12:12
    0 votes 5 comments
  • Funcotator and mutect2 coordinate system
    • Robert Bremel
    • September 28, 2020 17:19
    0 votes 7 comments
  • Call SNPs from mapped reads with MAPQ zero (bwa-mem, hg38, GATK4 Mutect2)
    • Juliab
    • September 27, 2020 20:47
    0 votes 4 comments
  • Mutect2 java.lang.NullPointerException Answered
    • Saskia
    • September 25, 2020 15:01
    0 votes 7 comments
  • Creating Panel of Normals Error
    • Vincent Appiah
    • September 25, 2020 14:54
    0 votes 3 comments
  • LeftAlignAndTrimVariants removes header tags
    • registered_user
    • September 22, 2020 08:03
    0 votes 1 comment
  • problem with docker image for Copy Number Alterations tutorial
    • Tatyana Zhuravleva
    • September 21, 2020 20:49
    0 votes 2 comments
  • Funcotator b38 and hg38 contig compatibility issue
    • Simon Lee
    • September 16, 2020 16:39
    0 votes 3 comments
  • Sample does not have a positive sample median when running DenoiseReadCounts
    • Andy Zhou
    • September 14, 2020 08:35
    0 votes 2 comments
  • GetPileupSummaries errors
    • Yuanyuan_Daisy Shen
    • September 11, 2020 05:52
    0 votes 1 comment
  • VariantAnnotator QualByDepth - no error and no annotation..
    • wiki97
    • September 09, 2020 10:09
    0 votes 10 comments
  • GenomeSTRiP analysis
    • Thandeka
    • September 08, 2020 14:30
    0 votes 3 comments
  • Combine GVCF htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Unexpected compressed block length
    • masagis
    • September 07, 2020 14:22
    0 votes 1 comment
  • Mutect errors
    • MPetlj
    • September 03, 2020 22:20
    0 votes 8 comments
  • GenomicsDBImport job does not complete, but gives no error
    • Lance Heady
    • September 03, 2020 20:36
    0 votes 3 comments
  • BedToIntervalList Error
    • Vincent Appiah
    • September 03, 2020 13:48
    0 votes 2 comments
  • Mutect2 (tumor & matched normal) - Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    • Lauren Eldershaw
    • September 02, 2020 05:36
    0 votes 2 comments
  • Can I run VQSR filter with individual chromosomes ?
    • Maíra R. Rodrigues
    • August 25, 2020 20:00
    0 votes 4 comments
  • Base Calibrator: A USER ERROR has occurred: Cannot read file: <file> because no suitable codecs found
    • Ana Isabel Castillo Orozco
    • August 24, 2020 16:49
    0 votes 1 comment
  • Terra module mutect2_pon (4.1.7.0) fails for large sample set (547 samples)
    • David Heiman
    • August 24, 2020 15:49
    0 votes 9 comments
  • mutect2-PoN creation
    • Yifat Geffen
    • August 21, 2020 14:52
    0 votes 3 comments
  • Does the VQSR approach cause any bias in data from isolated populations?
    • Renan
    • August 20, 2020 01:20
    0 votes 3 comments
  • Issues with Java heap space in CollectAllelicCounts
    • jejacobs23
    • August 18, 2020 22:52
    0 votes 12 comments
  • leftalignindels: java.lang.IllegalArgumentException: the range cannot contain negative indices
    • walawi
    • August 18, 2020 15:09
    0 votes 9 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 9 comments
  • Funcotator datasources.v1.7 gencode raise error
    • Tjitske de Vries
    • August 07, 2020 11:58
    0 votes 3 comments
  • HaplotypeCaller only produces .vcf.idx file not .vcf
    • Lance Heady
    • August 06, 2020 19:34
    0 votes 8 comments
  • Funcotator errors
    • MPetlj
    • August 05, 2020 23:40
    0 votes 27 comments
  • Incorrect alleles reported by Mutect2
    • Guruprasad Ananda
    • August 05, 2020 17:44
    • Edited
    0 votes 1 comment
  • Issue with output from CollectAllelicCounts
    • jejacobs23
    • August 04, 2020 22:01
    0 votes 1 comment
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