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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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Non-Human

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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • GenomicsDBimport not importing all the batches
    • Vinod Kumar
    • January 20, 2021 14:56
    • Edited
    0 votes 3 comments
  • haplotypecallerspark wants DS_Store
    • John Denton
    • January 14, 2021 14:53
    0 votes 6 comments
  • Missing samples from the output vcf file produced with GenotypeGVCFs
    • Patrícia H. Brito
    • January 08, 2021 11:41
    0 votes 5 comments
  • emit-ref-confidence error
    • Florence Morel
    • December 28, 2020 17:38
    0 votes 3 comments
  • the reads covering the special location between before HaplotypeCaller and after HaplotypeCaller
    • yunxin.f
    • December 23, 2020 08:51
    0 votes 1 comment
  • Genome STRiP - The output file of SVDiscovery is empty
    • latte kim
    • December 22, 2020 06:51
    0 votes 4 comments
  • REAL Variant not called by HaplotypeCaller
    • HASSAN BADRANE
    • December 15, 2020 23:45
    0 votes 1 comment
  • Error Creatting Dictionary for genome
    • Shazia Kunvar
    • December 15, 2020 12:19
    • Edited
    0 votes 1 comment
  • MarkDuplicatesSpark not working on Putty
    • Robinn Teoh
    • December 15, 2020 03:39
    • Edited
    0 votes 1 comment
  • Weird log of genotypeGVCF
    • Vinod Kumar
    • December 11, 2020 15:46
    0 votes 1 comment
  • Why is GenotypeGVCF taking a long time for a smaller genome?
    • Vinod Kumar
    • December 07, 2020 14:05
    • Edited
    0 votes 4 comments
  • Exclude-intervals error with PathSeq
    • Wir963
    • November 25, 2020 17:13
    0 votes 1 comment
  • How do I call germline variants with multiple samples -non human?
    • Jody Hey
    • November 20, 2020 16:15
    0 votes 2 comments
  • How do I choose GenotypeGVCFs parameters to best fit data from a selfing species with a highly duplicated genome?
    • JGi
    • November 16, 2020 12:57
    0 votes 1 comment
  • FixMateInformation does not solve ERROR:MATE_NOT_FOUND
    • Simon Hellemans
    • November 14, 2020 07:09
    • Edited
    1 vote 7 comments
  • AnalyzeCovaiates BQSR plots on canine data
    • Kate Megquier
    • November 13, 2020 22:14
    0 votes 3 comments
  • Disable strandbias
    • Wen Huang
    • November 13, 2020 20:34
    0 votes 1 comment
  • False positive Indel calling with GATK v4.1.4.0
    • ali pirani
    • November 12, 2020 15:14
    0 votes 1 comment
  • ApplyBQSR reduces reads quality
    • Khalil Jahed
    • November 11, 2020 21:46
    0 votes 3 comments
  • Getting an error with genomicsdbimport
    • Vinod Kumar
    • November 09, 2020 16:35
    • Edited
    0 votes 9 comments
  • How should I count the variation site for individual sample respectively from a multisample VCF?
    • Bingdi Liu
    • November 08, 2020 21:01
    0 votes 1 comment
  • Missing MQ scores in gvcf
    • Heather Tuttle
    • October 26, 2020 22:22
    0 votes 7 comments
  • Why does GATK haplotype caller calls SNPs from soft-clipped bases?
    • AlibiKr
    • October 13, 2020 14:46
    0 votes 1 comment
  • How to best use --phred-scaled-global-read-mismapping-rate
    • Andrea Ariani
    • October 07, 2020 12:14
    • Edited
    0 votes 1 comment
  • Access to outdated forum discussion
    • Begonia_pavonina
    • September 25, 2020 11:41
    0 votes 2 comments
  • Active Region Re-assembly
    • Ellen Weinheimer
    • September 21, 2020 14:54
    0 votes 1 comment
  • GenotypeGVCFs stalls while using --all-sites
    • Rachael Bay
    • September 15, 2020 22:13
    0 votes 18 comments
  • HaplotypeCaller for haploid genome
    • Pummi Singh
    • September 06, 2020 23:30
    0 votes 7 comments
  • ApplyBQSR to unmapped reads for non-model organism does not work with '-L unmapped' flag
    • cali
    • September 02, 2020 23:17
    0 votes 8 comments
  • No individual sample info in combineGVCF
    • Niyomi House
    • September 01, 2020 19:49
    0 votes 4 comments
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