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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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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
  • GQ=0 upstream of regions with no mapped reads
    • Frederik Valeur Seersholm
    • October 27, 2023 11:03
    0 votes 4 comments
  • Abnormal result from Haplotype caller using reduced representation bisulphite sequencing data
    • Jing Qi Chong
    • October 25, 2023 13:47
    • Edited
    0 votes 2 comments
  • HaplotypeCaller can't input the known variant from pooled samples
    • yangangli
    • September 17, 2023 04:18
    0 votes 2 comments
  • FastaAlternateReferenceMaker not replacing sites in fasta file
    • Melanie Wilkinson
    • August 10, 2023 02:10
    0 votes 11 comments
  • java.lang.ArrayIndexOutOfBoundsException: Index 32770 out of bounds for length 32770
    • Hanan Sela
    • August 06, 2023 09:07
    0 votes 3 comments
  • Annotate using funcotator
    • Rami Kheireddine
    • July 27, 2023 18:56
    0 votes 4 comments
  • how to use mutect2 for somatic variant calling among mouse tumor-only tissue (mm39)
    • yb87625
    • June 25, 2023 14:18
    0 votes 8 comments
  • HaplotypeCaller java.lang.ArrayIndexOutOfBoundsException: Index 32770 out of bounds for length 32770
    • Tiffany Kosch
    • June 19, 2023 22:31
    0 votes 4 comments
  • Question about bam format errors and handling large contigs
    • Tiffany Kosch
    • June 08, 2023 06:11
    0 votes 2 comments
  • VariantRecalibrator failing because no data found/Standard deviation of normal must be > 0 error despite running on whole genome data from ~900 samples
    • Annie Forster
    • June 06, 2023 12:28
    0 votes 2 comments
  • gatk-microbialmode.jar
    • Jian Wang
    • March 23, 2023 21:33
    1 vote 4 comments
  • known-sites for Felis_catus_9.0 (GCA_000181335.4) Answered
    • Vladimir Makarov
    • March 15, 2023 20:16
    0 votes 4 comments
  • How to remove strand bias from a virus-derived signal-end NGS dataset
    • Fadi Alnaji
    • March 02, 2023 08:26
    0 votes 4 comments
  • HaplotypeCaller not calling variants in the beginning of an alignment (except when --alleles is specified)
    • Bert Bogaerts
    • February 03, 2023 16:09
    0 votes 1 comment
  • Tribble never saw the required #CHROM header, but it is there for the program GenomicsDBImport
    • Zubayr Ahmad
    • January 23, 2023 17:08
    0 votes 2 comments
  • GATK HaplotypeCaller for non-model organism: gVCF output
    • Katie
    • January 12, 2023 18:17
    0 votes 0 comments
  • Somatic Variant Calling for a non-model species not finding any variants
    • Isabella Livingston
    • January 09, 2023 16:58
    0 votes 0 comments
  • GenotypeGVCF error
    • Akshaya Vasudevan
    • December 01, 2022 17:39
    • Edited
    0 votes 0 comments
  • The expected variants were not detected for pig RNA-seq by GATK
    • Wen-ye Yao
    • October 24, 2022 14:12
    • Edited
    1 vote 8 comments
  • GatherVcfs to concatenate GVCFs
    • sanjeevksh
    • October 22, 2022 00:38
    0 votes 3 comments
  • GenotypeGvcf tetraploids as diploids Answered
    • julien leuenberger
    • August 12, 2022 09:26
    0 votes 4 comments
  • GATK for Rnor6 - Funcotator error Answered
    • Ngoc Khoi Dang
    • August 03, 2022 16:30
    • Edited
    0 votes 1 comment
  • java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1 Answered
    • Zane Swaydan
    • June 30, 2022 11:38
    • Edited
    0 votes 8 comments
  • All intervals were filtered in Filterintervals
    • 侯旻
    • May 31, 2022 08:24
    0 votes 11 comments
  • FindBreakpointEvidenceSpark sudden shutdown Answered
    • Domniki Manousi
    • March 07, 2022 12:01
    0 votes 4 comments
  • emit-ref-confidence error Answered
    • Camila Martínez Avila
    • February 08, 2022 00:44
    0 votes 3 comments
  • gatk4-4.2.4.0-0 Fixmate Error Answered
    • Abrish
    • January 26, 2022 10:25
    • Edited
    0 votes 2 comments
  • GATK HaplotypeCaller disable filter -DF with the error in positional argument value Answered
    • Frans Dany
    • January 14, 2022 03:00
    0 votes 1 comment
  • VariantEval does not work or something wrong with my ref genome and dbsnps? Answered
    • Anh Mai
    • January 04, 2022 10:45
    0 votes 5 comments
  • ValidateSamFile Error Answered
    • Abrish
    • January 04, 2022 14:11
    • Edited
    0 votes 1 comment
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