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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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General Discussion

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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 produces empty VCF file but job doesn't fail
    • Fia
    • September 29, 2023 17:59
    • Edited
    0 votes 1 comment
  • Individual bwa, dict files, and tax files for bacteria, fungi, and viruses.
    • Caitlin Newman
    • September 27, 2023 15:27
    0 votes 0 comments
  • How to calculate the relative abundancy of microbes of a certain genus according to the output taxonomic file?
    • Siyao Zhang
    • September 27, 2023 11:44
    0 votes 0 comments
  • GenotypeGVCF by intervals emitted ALT allele at a missing site
    • GIULIA FABBRI
    • September 26, 2023 15:13
    0 votes 8 comments
  • Error in the second step when creating panel of normals : free(): invalid pointer
    • Ariadna Acedo
    • September 26, 2023 10:21
    0 votes 5 comments
  • FilterMutectCalls - unfiltered.vcf.stats file not found
    • Fia
    • September 26, 2023 04:03
    0 votes 2 comments
  • DRAGEN-GATK and joint genotyping
    • Le Qi
    • September 26, 2023 02:09
    • Edited
    0 votes 3 comments
  • Mutect2 MBQ correction of pcr overlapping in UMI reads
    • Warren
    • September 21, 2023 10:21
    0 votes 1 comment
  • How long will gatk PathSeqPipelineSpark run?
    • Siyao Zhang
    • September 18, 2023 12:47
    0 votes 0 comments
  • GATK suddenly exit without error message
    • Siyao Zhang
    • September 18, 2023 03:58
    0 votes 1 comment
  • T2T
    • 自然卷
    • September 15, 2023 10:01
    0 votes 3 comments
  • GATK haplotype variant calling on ONT amplicons gives empty VCF with headers.
    • Aswini
    • September 11, 2023 23:14
    0 votes 1 comment
  • Mutect2 heteroplasmy sensitivity
    • BM
    • September 06, 2023 10:43
    0 votes 1 comment
  • CNNScoreVariants, python timeout error occurred
    • Henry
    • September 08, 2023 01:22
    • Edited
    0 votes 7 comments
  • MergeBamAlignment Error - java.lang.IllegalArgumentException Answered
    • Fia
    • August 31, 2023 18:27
    0 votes 8 comments
  • AnalyzeSaturationMutagenesis behavior with disjoint pairs
    • chris m
    • August 28, 2023 14:48
    0 votes 6 comments
  • cutting down on db or fa file based off of .txt results in pathseqspark
    • caitlin newman
    • August 24, 2023 22:09
    0 votes 1 comment
  • GATK 4.2.5.0 = which version of Java or other requirements? Answered
    • David A Bird
    • August 22, 2023 20:14
    0 votes 2 comments
  • Reinstall GATK4
    • 김콩순
    • August 21, 2023 06:49
    0 votes 1 comment
  • Question regarding funcotator datasets
    • robert dubin
    • August 18, 2023 19:33
    0 votes 2 comments
  • A USER ERROR has occurred: Invalid argument 'hg38.fa'.
    • 김콩순
    • August 16, 2023 05:12
    0 votes 3 comments
  • gtf file for hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta
    • Fiona Liang
    • August 12, 2023 06:18
    0 votes 1 comment
  • What's the right order of Mitochondrial pipeline
    • Fiona Liang
    • August 12, 2023 04:05
    0 votes 5 comments
  • Novaseq X - OPTICAL_DUPLICATE_PIXEL_DISTANCE
    • G E
    • August 12, 2023 03:17
    0 votes 1 comment
  • GenomicsDBImport for joint genotyping Answered
    • anr
    • August 11, 2023 17:18
    0 votes 3 comments
  • ExtractIlluminaBarcodes not using more than 1 cpu
    • Priscilla Glenn
    • August 09, 2023 15:28
    0 votes 11 comments
  • Mitochondrial LiftoverVcf
    • Fiona Liang
    • August 07, 2023 02:05
    0 votes 2 comments
  • How to find unique variants among individual-level VCF files?
    • Ray
    • August 05, 2023 18:32
    0 votes 3 comments
  • Pipeline for germline, short variant discovery in targeted sequencing data
    • Rebeka Bató
    • August 30, 2023 08:50
    • Edited
    0 votes 3 comments
  • Picard CollectInsertSizeMetrics 3.1.0 doesn't find R
    • Craig Amundsen
    • August 01, 2023 23:18
    • Edited
    0 votes 4 comments
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