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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 no status All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • get the basics for Haplotypecaller
    • Maarten Nijenhuis
    • June 02, 2023 10:37
    0 votes 0 comments
  • STAR and GATK RNAseq based SNP detection
    • Jahn Davik
    • May 03, 2023 08:14
    0 votes 0 comments
  • Best practice with read groups
    • Sheryl
    • April 27, 2023 00:43
    0 votes 1 comment
  • Download GATK4 required packages in docker container
    • Marcela Martinez
    • April 25, 2023 22:29
    0 votes 1 comment
  • Is It Allowed To Submit An Entire Code For Review?
    • Y R
    • April 23, 2023 10:09
    0 votes 2 comments
  • Call input and runtime attributes evaluation failed for PairedFastQsToUnmappedBAM
    • Ananya Saji
    • April 21, 2023 06:29
    0 votes 0 comments
  • Running GenomicsDBImport/CombineGVCFs on Azure leads to User Error: Illegal argument value
    • Martin Danner
    • April 18, 2023 10:29
    • Edited
    0 votes 1 comment
  • Mutect2 PON
    • Sheryl
    • April 17, 2023 04:28
    0 votes 1 comment
  • BaitDesigner Fasta Output Missing Gene Names
    • Tapoka M
    • April 12, 2023 10:27
    0 votes 1 comment
  • HaplotypeCaller produces VCF's from 1KG data that have low SNP overlap
    • Nils Paffen
    • April 11, 2023 09:00
    • Edited
    0 votes 1 comment
  • Interval list and the “Mate not found” error in WES data
    • LY Wang
    • April 07, 2023 13:19
    0 votes 2 comments
  • Steps For GATK-gCNV pipleline on Exome Data
    • Y R
    • April 03, 2023 15:30
    • Edited
    0 votes 12 comments
  • Haplotype caller error "Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class"
    • Anna Gatseva
    • March 22, 2023 11:00
    0 votes 1 comment
  • somatic CNV PoN
    • Sheryl
    • March 06, 2023 20:00
    • Edited
    0 votes 1 comment
  • Mutect2 wdl interval list and scatter count
    • Sheryl
    • March 06, 2023 02:19
    • Edited
    0 votes 3 comments
  • gatk HaplotypeCaller generates Excessive Heterozygous SNPs in inbred lines
    • Mahmood Hasan
    • February 24, 2023 19:27
    0 votes 0 comments
  • ApplyBQSR
    • Wondessen Ayalew
    • February 23, 2023 06:19
    0 votes 10 comments
  • GATK configration
    • Wondessen Ayalew
    • February 13, 2023 12:28
    0 votes 5 comments
  • MarkDuplicatesSpark Error
    • Yosra Bejaoui
    • February 08, 2023 06:25
    0 votes 1 comment
  • Genotype and AD in Mutect2 vcf output
    • Ester Feldmesser
    • February 02, 2023 13:56
    0 votes 1 comment
  • Genome sequence analysis: preprocessing to variant analysis
    • Nagarajan Raju
    • January 24, 2023 16:13
    0 votes 0 comments
  • Is there a way to preserve numeric genotypes with VariantsToTable?
    • Ben Sprung
    • January 11, 2023 18:16
    0 votes 2 comments
  • VariantFiltration Issue
    • Ethan Mattice
    • January 04, 2023 17:57
    0 votes 1 comment
  • Markduplicates
    • Atal Saha
    • January 03, 2023 16:55
    0 votes 5 comments
  • Scatter Gather principle by chromosome on Gatk
    • Sushant Sawant
    • November 28, 2022 06:44
    • Edited
    1 vote 2 comments
  • Where can I download Homo_sapiens_assembly38.haplotype_database.txt
    • Sheryl
    • November 17, 2022 05:36
    0 votes 2 comments
  • no gatk installation
    • pedro toruno
    • October 04, 2022 19:18
    0 votes 0 comments
  • Multi-library designs: error proceeding from pre-processing to variant calling
    • Sabrina McNew
    • August 23, 2022 20:35
    0 votes 1 comment
  • GenomicsDB Import issues
    • aheritas
    • July 15, 2022 15:47
    0 votes 1 comment
  • Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
    • Joel Wallenius
    • May 02, 2022 10:38
    0 votes 1 comment
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