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<prev • 931 results • page 1 of 32 • next >
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A USER ERROR has occurred: Positive training model failed to converge.
vcf gatk max-gaussians written 23 hours ago by dare_devil • 1.3k
14
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3
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125
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7 follow
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Is it possible to run haplotypecaller in gnu parallel ?
haplotypecaller gatk parallel gnu parallel written 3 days ago by dare_devil • 1.3k
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102
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About GATK4 Mutect2 runtime (Whole Exome seq)
gatk whole exome sequencing mutect2 written 3 days ago by kwanghoon • 20
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39
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Calculating Allele Balance in GATK4
gatk written 3 days ago by MAPK • 1.7k
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1
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74
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5 follow
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Recalibrating variants in GATK4.1 as compared to GATK3.7
gatk snp written 4 days ago by vinayjrao • 200 • updated 4 days ago by dare_devil • 1.3k
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90
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6 follow
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CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
trio gatk calculategenotypeposteriors ped written 5 days ago by dare_devil • 1.3k
12
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3
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110
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7 follow
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Combine two VCF files with GATK4
gatk written 6 days ago by MAPK • 1.7k • updated 6 days ago by svp • 420
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6 follow
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How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
vqsr variantrecalibrator gatk written 7 days ago by dare_devil • 1.3k
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65
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MergeVcfs vs GatherVCFs in GATK 4
gatk written 8 days ago by MAPK • 1.7k
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WARN in GATK HaplotypeCaller
haplotypecaller gatk snp written 2.8 years ago by Siavash Salek Ardestani • 20 • updated 10 days ago by Biostar ♦♦ 20
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1
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71
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1
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fastq processing with parallel command
bioinformatics fastq parallel gatk written 11 days ago by SurdanBurasi • 0 • updated 11 days ago by ATpoint ♦ 44k
2
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1
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90
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1
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GATK BaseRecalibrator error.. how do I solve this?
gatk ngs wes written 12 days ago by kwanghoon • 20 • updated 11 days ago by Pierre Lindenbaum ♦ 133k
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65
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Different dbSNP files input yield different variants?
gatk dbsnp snp mutect2 written 14 days ago by Ash • 10
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108
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7 follow
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Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
trio gatk genomicsdbimport cohort written 15 days ago by dare_devil • 1.3k
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GATK BaseRecalibrator error: input files reference and features have incompatible contigs
gatk baserecalibrator written 15 days ago by ben.ponv • 0
2
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1
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80
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1
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How to call denovo variants from multiple trios cohort?
trio gatk denovo germline written 15 days ago by dare_devil • 1.3k • updated 15 days ago by Pierre Lindenbaum ♦ 133k
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93
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High CPU of GATK and Picard programs
gatk java ram cpu written 16 days ago by ognjen011 • 200
2
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1
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132
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1
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GATK read groups for instruments from BGI Tech like BGISEQ-500?
gatk written 20 days ago by MatthewP • 850 • updated 19 days ago by vdauwera • 990
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104
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which tool should be used to call the genotype?
gatk ngs genotype calling variant genotype written 20 days ago by JENNIE • 0
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Merging genomic databases from different intervals (GenomicsDBImport)
gatk written 20 days ago by raf.marcondes • 40
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92
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Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mouse mutect snp baserecalibrator written 21 days ago by Ash • 10
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1
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114
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1
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the number of the reads covering the snp after HaplotypeCaller
haplotypecaller gatk snp depth written 4 weeks ago by 543541656 • 20 • updated 4 weeks ago by Pierre Lindenbaum ♦ 133k
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138
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0
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GATK markduplicates / applyBQSR / haplotypecaller tools support unix pipe?
gatk unix pipe markduplicates applybqsr written 8 weeks ago by roccostorace • 30 • updated 4 weeks ago by Biostar ♦♦ 20
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131
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1
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GATK Exome PON
gatk snp mutect2 written 5 weeks ago by chimerajit • 0
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131
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Optimal Number of SNPs in NA12878 WES Data
gatk wes snp written 5 weeks ago by hkarakurt • 100
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1
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130
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1
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Considerations when merging a gVCF with a VCF?
vcf gatk wes bcftools gvcf written 5 weeks ago by jon.klonowski • 70 • updated 5 weeks ago by kreenaijuriya • 0
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191
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ReadsPipelineSpark marking duplicates differently than MarkDuplicates
gatk dna-seq alignment written 6 weeks ago by from the mountains • 110
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1
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162
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1
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How to speed up the GenotypeGVCF?
gatk genotypegvcf written 6 weeks ago by kumar.vinod81 • 280 • updated 6 weeks ago by Pierre Lindenbaum ♦ 133k
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VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
gatk written 2.5 years ago by Ana • 180 • updated 7 weeks ago by Christopher Walker • 50
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114
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monozygotic twins ped file specification
gatk pedigree twin ped written 7 weeks ago by cocchi.e89 • 120
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