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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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  • Error loading filtermutectcalls.var.vcf.gz in IGV 2.16.0 - htsjdk.samtools.util.RuntimeIOException [file] has invalid uncompressedLength
    • Matteo Costacurta
    • April 12, 2023 23:16
    0 votes 1 comment
  • GaTK-3.3-0 download
    • Walter Tulle
    • March 30, 2023 14:31
    0 votes 2 comments
  • Error in Running command GtcToVcf
    • Nur Adlina Binti Mohd Affian
    • March 29, 2023 05:28
    0 votes 4 comments
  • Question about the allele depth generated by haplotypecaller and ASEReadCounter
    • 杨烁
    • March 27, 2023 09:00
    0 votes 1 comment
  • FastaAlternateReferenceMaker generates same sequence for multisample vcf
    • Kathrin B
    • March 17, 2023 14:09
    0 votes 1 comment
  • GATK ContaminationModel
    • Itai Beno
    • March 15, 2023 16:36
    0 votes 0 comments
  • Error while running HaplotypeCaller
    • Achint Kumar
    • February 19, 2023 13:54
    0 votes 1 comment
  • Picard LiftOver behaviour for multiallelic positions
    • Adeline Morez
    • February 03, 2023 11:22
    0 votes 1 comment
  • ASEReadCounter does not return the value only for chrX
    • Kei Enomoto
    • February 04, 2023 05:07
    • Edited
    0 votes 2 comments
  • ApplyVQSR: "[W::bgzf_read_block] EOF marker is absent" and "[tabix] the index file exists." errors
    • Bob Ye
    • January 25, 2023 23:12
    0 votes 0 comments
  • Liftover Picard hg19 to hg38: variants were not successfully lifted over
    • Andres Caballero
    • December 09, 2022 18:39
    2 votes 2 comments
  • gatk4-GenotypeGVCFs.nf doens't recognize Primary_000001F chromosomes for process GatherVcfs
    • Carole Couture
    • December 08, 2022 15:19
    0 votes 0 comments
  • Invalid or corrupt jarfile error Answered
    • Benjamin Singer
    • November 30, 2022 00:55
    • Edited
    0 votes 2 comments
  • HaplotypeCaller confuses introns as long deletions
    • Vladimir Souza
    • November 09, 2022 23:03
    • Edited
    0 votes 4 comments
  • error when running ASEReadCounter
    • behzad
    • October 27, 2022 11:20
    0 votes 2 comments
  • SortSam - Question about I/O error
    • Henry
    • October 27, 2022 08:20
    0 votes 2 comments
  • ShiftFasta creates empty intervals file Answered
    • Ram
    • October 21, 2022 07:56
    • Edited
    0 votes 4 comments
  • Does GATK4 BaseRecalibrator not understand relative paths?
    • Eva (Evander)
    • October 17, 2022 12:51
    0 votes 10 comments
  • CombineGVCFs - possible to restart/continue run?
    • medgen
    • October 11, 2022 14:01
    0 votes 5 comments
  • Error in Running command CreateExtendedIlluminaManifest Answered
    • Nur Adlina Binti Mohd Affian
    • October 03, 2022 09:21
    0 votes 3 comments
  • CGA3_WES_Characterization_Pipeline_v0.2_Jun2019 PoN Errors...
    • Rose Gold
    • September 28, 2022 14:32
    0 votes 1 comment
  • How can I build the GATK jar so that the intel native libraries are available? Answered
    • Mark Schreiber
    • September 22, 2022 16:49
    0 votes 4 comments
  • GenomeSTRiP SVPreprocess error
    • Jibin Jeong
    • September 15, 2022 04:51
    • Edited
    1 vote 1 comment
  • libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow Answered
    • Marta Giovalli
    • September 14, 2022 12:47
    • Edited
    0 votes 4 comments
  • VCF input example Answered
    • Noam Rudberg
    • August 07, 2022 09:45
    0 votes 1 comment
  • Cannot use haplotype caller on STAR-aligned data Answered
    • David Condon
    • August 05, 2022 15:49
    0 votes 2 comments
  • MergeVcfs issue: Illegal character in fragment at index 1: ##fileformat=VCFv4.2 Answered
    • Liyang Zhang
    • August 03, 2022 08:02
    • Edited
    0 votes 2 comments
  • FindBadGenomicKmersSpark running indefinitely Answered
    • Cher Wei Yuan
    • August 02, 2022 02:25
    0 votes 5 comments
  • Using the IndexFeatureFile, doesn't recognize -F flag Answered
    • Gijs C
    • July 30, 2022 12:21
    0 votes 2 comments
  • GenomicsDBImport works in interactive shell, but not in a script Answered
    • Guy Shapira
    • July 21, 2022 22:05
    0 votes 1 comment
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