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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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New User Advice

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Show all All Planned Not planned Completed Answered No status Sort by newest post Newest post Recent activity Votes Comments
  • somatic CNV PoN
    • Sheryl
    • March 06, 2023 20:00
    • Edited
    0 votes 0 comments
  • 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 3 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
  • Unclear why Picard ValidateSamFile is producing an error Answered
    • LOIC TALIGNANI
    • November 15, 2022 09:51
    0 votes 6 comments
  • CollectSamErrorMetrics error Answered
    • Joe Georgeson
    • October 10, 2022 17:41
    0 votes 3 comments
  • no gatk installation
    • pedro toruno
    • October 04, 2022 19:18
    0 votes 0 comments
  • VariantFiltration issue Answered
    • Theresa Saunders
    • September 09, 2022 20:41
    0 votes 3 comments
  • Multi-library designs: error proceeding from pre-processing to variant calling
    • Sabrina McNew
    • August 23, 2022 20:35
    0 votes 1 comment
  • Find rate of homozygosity Answered
    • Joyce Anon
    • July 28, 2022 05:12
    0 votes 4 comments
  • GenomicsDB Import issues
    • aheritas
    • July 15, 2022 15:47
    0 votes 1 comment
  • Package ‘gsalib’ was removed from the CRAN repository. Answered
    • igor
    • July 13, 2022 15:56
    0 votes 3 comments
  • Proper way to prepare .bam for MarkDuplicatesSpark Answered
    • samuel
    • July 06, 2022 06:46
    1 vote 3 comments
  • A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered
    • Maha Tageldein
    • June 06, 2022 05:03
    0 votes 5 comments
  • GenomicsDBImport - why "intervals" is required?? Answered
    • Jianying Li
    • May 25, 2022 00:39
    0 votes 3 comments
  • Gatk4 rnaseq germline snps indels json file Answered
    • Alan Foley
    • May 19, 2022 10:29
    • Edited
    0 votes 3 comments
  • Variant Quality Score Recalibration Answered
    • Jakub S
    • May 09, 2022 15:27
    0 votes 3 comments
  • How to use WGA Data in picard Answered
    • Marcus Varni
    • May 03, 2022 23:13
    0 votes 3 comments
  • Suggestions to find pathogenic variant Answered
    • Joyce Anon
    • May 03, 2022 20:57
    0 votes 4 comments
  • Cromwell configuration problem: "No configuration setting found for key 'job-id-regex'"
    • Joel Wallenius
    • May 02, 2022 10:38
    0 votes 1 comment
  • Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered
    • Joyce Anon
    • April 25, 2022 06:30
    0 votes 20 comments
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