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Genome Analysis Toolkit

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 answered All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered
    • KATHIE NGO
    • August 27, 2020 17:31
    • Edited
    0 votes 9 comments
  • Liftover Picard hg19 to hg38: variants were not successfully lifted over Answered
    • Andres Caballero
    • December 09, 2022 18:39
    2 votes 3 comments
  • GATK Index Feature FIle No suitable codecs found Answered
    • Y R
    • August 29, 2023 15:32
    • Edited
    0 votes 4 comments
  • Install GATK version 4.1.0.0 using Conda. Answered
    • dongju
    • August 29, 2023 08:32
    0 votes 4 comments
  • BaseRecalibrator on MT .bam files Answered
    • Sharon Cox
    • February 19, 2021 09:48
    • Edited
    0 votes 5 comments
  • evaluation of the VCF file which is made using GATK Answered
    • behzad
    • June 22, 2020 11:41
    0 votes 6 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
  • Invalid or corrupt jarfile error Answered
    • Benjamin Singer
    • November 30, 2022 00:55
    • Edited
    0 votes 2 comments
  • ShiftFasta creates empty intervals file Answered
    • Ram
    • October 21, 2022 07:56
    • Edited
    0 votes 4 comments
  • Error in Running command CreateExtendedIlluminaManifest Answered
    • Nur Adlina Binti Mohd Affian
    • October 03, 2022 09:21
    0 votes 3 comments
  • Accessing the resource bundle. Answered
    • nagam surya
    • June 28, 2022 18:35
    0 votes 6 comments
  • 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
  • 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
  • How to run muTect without normal sample? Answered
    • Yingjie Zhu
    • July 11, 2022 21:35
    1 vote 3 comments
  • VCF input example Answered
    • Noam Rudberg
    • August 07, 2022 09:45
    0 votes 1 comment
  • GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
    • Nils Homer
    • August 06, 2020 00:13
    1 vote 9 comments
  • Cannot use haplotype caller on STAR-aligned data Answered
    • David Condon
    • August 05, 2022 15:49
    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
  • Haploytpe caller shows me that 0 read(s) were filtered by: MappingQualityAvailableReadFilter etc. Answered
    • pb
    • July 13, 2022 14:15
    0 votes 4 comments
  • MarkduplicatesSpark failed Answered
    • lid.zigh
    • November 23, 2021 13:44
    0 votes 5 comments
  • markDuplicatesSpark running out of memory Answered
    • Matt Snyder
    • June 09, 2022 19:34
    0 votes 3 comments
  • Hard filters on VariantFiltration following HaplotypeCaller; Filter contains an illegal character Answered
    • Graeme Thorn
    • May 27, 2022 21:05
    • Edited
    0 votes 5 comments
  • Refseq accession number and version number in Funcotator Answered
    • TMB
    • April 26, 2022 04:13
    0 votes 4 comments
  • No results of CollectvariantCallingMetrics Answered
    • Yenan
    • November 30, 2020 07:13
    0 votes 30 comments
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 13 comments
  • CNNScoreVariants Issues with environment and Java version Answered
    • Kathrin B
    • April 13, 2022 15:07
    • Edited
    0 votes 6 comments
  • ApplyBQSR no positional argument is defined for this tool Answered
    • Jose Aragon
    • March 06, 2021 14:26
    0 votes 7 comments
  • Fontconfig error in the newest gatk docker image Answered
    • SkyWarrior
    • April 10, 2022 09:02
    • Edited
    0 votes 1 comment
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