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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 votes Newest post Recent activity Votes Comments
  • Liftover Picard hg19 to hg38: variants were not successfully lifted over
    • Andres Caballero
    • December 09, 2022 18:39
    2 votes 2 comments
  • Do I need to perform fastqc and adapters trimming before gatk pipeline?
    • LG
    • May 01, 2020 02:49
    2 votes 4 comments
  • Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH
    • Jose Arcadio Buendia
    • February 28, 2020 01:53
    • Edited
    2 votes 2 comments
  • Known issue: old GATK forum inaccessible Answered
    • Tiffany Miller
    • January 23, 2020 17:47
    • Edited
    2 votes 3 comments
  • Any automatic downloadable gatk3?
    • ale
    • January 09, 2020 13:16
    2 votes 13 comments
  • GenomeSTRiP SVPreprocess error
    • Jibin Jeong
    • September 15, 2022 04:51
    • Edited
    1 vote 1 comment
  • How to run muTect without normal sample? Answered
    • Yingjie Zhu
    • July 11, 2022 21:35
    1 vote 3 comments
  • Genomestrip: Argument with name '--ploidyMapFile' (-ploidyMapFile) is missing
    • Senwei
    • April 27, 2022 07:59
    1 vote 2 comments
  • Error in GenomicsDBImport: Invalid deflate block found Answered
    • Lauren Hennelly
    • February 26, 2022 20:26
    1 vote 6 comments
  • HaplotypeCaller -ERC GVCF -variant_index_type LINEAR
    • Matilde
    • January 22, 2021 18:22
    1 vote 1 comment
  • How do I rename output folder created using glob (WDL-Cromwell)?
    • Mar Quiroga
    • November 25, 2020 23:20
    1 vote 1 comment
  • GenomicsDBImport: Attempting to genotype more than 50 alleles Answered
    • Nils Homer
    • August 06, 2020 00:13
    1 vote 9 comments
  • GenomicsDBImport: has too many genotypes in the combined VCF record
    • Nils Homer
    • August 06, 2020 00:12
    • Edited
    1 vote 2 comments
  • Warning: Reading will be unbuffered. Answered
    • Linda Do
    • July 06, 2020 16:35
    1 vote 3 comments
  • Merge different individual VCF
    • Linda Do
    • July 06, 2020 07:05
    1 vote 11 comments
  • Picard CollectHsMetrics PCT_EXC_OFF_TARGET
    • Holly Corbitt
    • May 07, 2020 04:09
    1 vote 4 comments
  • Problem Installing and testing GATK-4.1.7.0
    • Arjun Upadhaya
    • May 04, 2020 06:34
    1 vote 5 comments
  • jar for mutect 1.1.7
    • Knight Ni
    • April 19, 2020 17:08
    1 vote 6 comments
  • Panel of Normals Documentation Answered
    • Ryan Gimple
    • April 16, 2020 17:48
    1 vote 16 comments
  • GATK/Picard does not detect mates in paired-end BAM
    • jipvdinter
    • April 07, 2020 11:34
    • Edited
    1 vote 3 comments
  • HaplotypeCaller produces very large .idx files
    • Anze Staric
    • February 20, 2020 20:30
    1 vote 4 comments
  • ValidateSamFile behavior
    • Robert Edgar
    • February 17, 2020 18:07
    1 vote 7 comments
  • Problem Installing GATK python environment - SOLUTION POSTED! Featured
    • SkyWarrior
    • February 06, 2020 07:21
    • Edited
    1 vote 17 comments
  • Typos in docs
    • Andrea Haessly
    • January 29, 2020 20:47
    1 vote 1 comment
  • CNNScoreVariants carshes with java.lang.NullPointerException Answered
    • riederd
    • January 17, 2020 15:29
    1 vote 13 comments
  • MarkDuplicatesSpark crash
    • David Gómez-Sánchez
    • January 07, 2020 17:02
    1 vote 10 comments
  • GaTK-3.3-0 download
    • Walter Tulle
    • March 30, 2023 14:31
    0 votes 0 comments
  • Error in Running command GtcToVcf
    • Nur Adlina Binti Mohd Affian
    • March 29, 2023 05:28
    0 votes 1 comment
  • 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 0 comments
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