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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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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
  • what is a Good Cigar?
    • chenglei
    • July 02, 2022 06:25
    0 votes 2 comments
  • BQSR workflow for non-model organism
    • Julia Lopez Delgado [RPG]
    • June 28, 2022 12:30
    0 votes 1 comment
  • HaplotypeCaller not working for sort bam files
    • Alok Tantuway
    • June 27, 2022 12:34
    0 votes 2 comments
  • CalculateContamination inputs for paired tumor-normal data
    • Robin Mjelle
    • June 25, 2022 15:04
    0 votes 2 comments
  • HaplotypeCaller calling whole chromosome as NON_REF
    • Tommy Phannareth
    • June 20, 2022 14:43
    0 votes 1 comment
  • GATK CNV caller cohort mode long running
    • Anjali Kumari
    • June 16, 2022 11:33
    0 votes 2 comments
  • How to identify differential microsatellites in GATK ?
    • Arye Harel
    • June 15, 2022 08:27
    • Edited
    0 votes 1 comment
  • Variant Filtering problem after merging
    • Juan Pablo Aguilar Cabezas
    • June 11, 2022 23:56
    • Edited
    0 votes 1 comment
  • GATK Handling of Paralogs
    • Morgan Sparks
    • June 01, 2022 18:25
    0 votes 1 comment
  • Mutect2 Variant Filters
    • Lynn Loy
    • May 31, 2022 12:38
    0 votes 2 comments
  • No Pileup Tables Answered
    • Wesley Kwong
    • May 25, 2022 16:20
    0 votes 16 comments
  • GenomicsDBImport Answered
    • Ali Basuony
    • May 22, 2022 23:22
    • Edited
    0 votes 3 comments
  • Joint calling a mixed cohort (WES and WGS )
    • Ali Saadat
    • May 21, 2022 13:06
    0 votes 1 comment
  • Differences between GATK 3.5 and 4.2.5
    • Luis Willian Pacheco Arge
    • May 18, 2022 13:37
    0 votes 1 comment
  • Mutect2 calling 0/1 genotypes at sites with no reference base calls
    • Eppie Jones
    • May 18, 2022 11:05
    0 votes 1 comment
  • Differentiating variant site from Force call or de novo
    • Kevin Nathanael Ramanto
    • May 18, 2022 04:34
    0 votes 2 comments
  • picard CompareSAMs
    • Matt Snyder
    • May 17, 2022 23:25
    • Edited
    0 votes 1 comment
  • problem with GATK ASEReadCounter
    • behzad
    • May 17, 2022 14:45
    0 votes 4 comments
  • Using the folded site frequency spectrum as --input-prior option in GenotypeGVCFs
    • Emma Howell
    • May 16, 2022 17:50
    0 votes 1 comment
  • Mutect2 size of indels detected?
    • rose froehlich
    • May 11, 2022 15:08
    0 votes 1 comment
  • Recommended tool for obtaining thresholded covered genomic regions
    • Philipp Hähnel
    • May 11, 2022 14:58
    0 votes 2 comments
  • Mutations in contiguous sites within a sample
    • ashgorden
    • May 10, 2022 14:37
    0 votes 4 comments
  • DepthOfCoverage: does --gene-list honour restrictions set by --intervals? Answered
    • Gordon Blackshields
    • May 05, 2022 13:39
    0 votes 2 comments
  • HAPLOTYPE_MAP in CrosscheckFingerprints (Picard)
    • dhwani
    • May 04, 2022 12:42
    0 votes 2 comments
  • FastqToSam gives me wrong output for read pairs Answered
    • Bastiaan Tjeng
    • May 02, 2022 16:43
    0 votes 4 comments
  • Mutect2 bamout reports deletion reads, but VCF calls out the next base following deletion position rather than directly reporting deletion mutation Answered
    • CYWang
    • May 01, 2022 15:50
    0 votes 3 comments
  • CombineGVCFs-VCFHeader Answered
    • xieguangting
    • April 28, 2022 05:12
    0 votes 2 comments
  • Why is the tumor in the column after normal when I call variants with Mutect2 in tumor-normal matched model? I have used mutect2 for six years ,but this have never happened. The following is my command: Answered
    • can wang
    • April 26, 2022 20:54
    0 votes 4 comments
  • BaseRecalibrator--known-sites Answered
    • xieguangting
    • April 25, 2022 14:06
    0 votes 2 comments
  • GATK Mutect2 PON mus musculus vcf file conversion Answered
    • Yana Vassileva
    • April 26, 2022 06:25
    • Edited
    0 votes 2 comments
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