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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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  • HaplotypeCaller bam file path not recognized
    • Phillip Morin - NOAA Federal
    • March 13, 2020 18:42
    0 votes 7 comments
  • I want to know sequence_group_intervals in fivedollar-genome-anlalysis pipeline
    • BI_joy
    • March 11, 2020 08:53
    • Edited
    0 votes 1 comment
  • Do BQSR ignore VCF sites marked as filtered, or must they be removed from the file?
    • mk
    • March 11, 2020 00:37
    0 votes 4 comments
  • Dockerfile for genomes-in-the-cloud
    • Tony Bendis
    • March 10, 2020 05:16
    0 votes 5 comments
  • error java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Byte
    • BI_joy
    • March 02, 2020 12:16
    0 votes 1 comment
  • CreateSomaticPanelOfNormals fails
    • Dieter Best
    • February 28, 2020 23:46
    0 votes 2 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
  • Why does my vcf contain a genotype when there are no reads supporting it?
    • Jeff Duty
    • February 27, 2020 14:51
    • Edited
    0 votes 3 comments
  • Delete <NON_REF> from VCF
    • ValeriyaVS
    • February 26, 2020 08:02
    0 votes 2 comments
  • Cohort vcf WES analysis
    • Surdan Burasi
    • February 25, 2020 12:44
    0 votes 1 comment
  • Where did the GATK3 documentation go?
    • jejacobs23
    • February 24, 2020 20:20
    0 votes 1 comment
  • Has -log_to_file been depreciated
    • Wanda Sankey
    • February 24, 2020 18:12
    0 votes 1 comment
  • Fail to set up conda environment for GATK with the gatkcondaenv.yml file
    • fanwayne
    • February 24, 2020 12:16
    0 votes 5 comments
  • Question: Picard - MergeBamAlignment: Reads remaining on alignment iterator
    • Nguyen Nguyen Thanh
    • February 23, 2020 15:03
    0 votes 4 comments
  • HaplotypeCaller produces very large .idx files
    • Anze Staric
    • February 20, 2020 20:30
    1 vote 4 comments
  • What kind of statistical methods genome strip used?
    • zhangwusheng
    • February 19, 2020 18:21
    0 votes 3 comments
  • HaplotypeCaller complains (in 2 different ways) about sample-name
    • Terry Jones
    • February 18, 2020 14:07
    0 votes 12 comments
  • Problem running GenomeSTRiP CNVDiscovery on X chromosome
    • Laura Cottino
    • February 18, 2020 09:00
    0 votes 5 comments
  • BI and BD tags.
    • Semen Leyn
    • February 17, 2020 19:44
    0 votes 2 comments
  • ValidateSamFile behavior
    • Robert Edgar
    • February 17, 2020 18:07
    1 vote 7 comments
  • WES covarage analysis
    • Surdan Burasi
    • February 16, 2020 21:09
    0 votes 4 comments
  • <b>OUT OF OFFICE NOTICE</b>: GATK Team on holiday on Feb 17th 2020
    • Bhanu Gandham
    • February 15, 2020 18:20
    0 votes 0 comments
  • User error: input files reference and features have incompatible contigs
    • mons7re
    • February 14, 2020 14:12
    0 votes 6 comments
  • Loss of data after HaplotypeCaller
    • mbesskd5
    • February 14, 2020 10:14
    • Edited
    0 votes 5 comments
  • What is the 'physical phasing'
    • whynot
    • February 13, 2020 04:29
    0 votes 3 comments
  • Cannot get AddOrReplaceReadGroups to run
    • Robert Butler
    • February 12, 2020 21:20
    0 votes 2 comments
  • Where's the DRAGEN?
    • Matthias De Smet
    • February 11, 2020 08:29
    0 votes 3 comments
  • PathseqPipelineSpark stops without error message
    • vitor heidrich
    • February 07, 2020 00:44
    0 votes 6 comments
  • GATK on Oracle Cloud Infrastructure
    • Marcelo Bicudo
    • February 06, 2020 21:18
    0 votes 2 comments
  • Problem Installing GATK python environment - SOLUTION POSTED! Featured
    • SkyWarrior
    • February 06, 2020 07:21
    • Edited
    1 vote 17 comments
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