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4
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84
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GATK failing to find any variants - how to troubleshoot?
gatk rna-seq written 2 days ago by Kristin Muench • 390
0
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1
answer
55
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1
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Genotype file supporting gatk CalculateGenotypePosteriors
wgs gatk genotyping written 12 days ago by gwotto • 0
1
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1
answer
46
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1
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snp identification with Haplotypecaller and SelectVariants
gatk snp written 4 days ago by felipead66 • 20 • updated 4 days ago by Pierre Lindenbaum ♦ 118k
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1
answer
64
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6 follow
1
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VariantFiltration warning "undefined variable"
gatk variantfiltration error written 5 days ago by felipead66 • 20 • updated 5 days ago by Pierre Lindenbaum ♦ 118k
3
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68
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GATK HaplotypeCaller Problems
software error gatk next-gen alignment written 6 days ago by chengye • 0
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1
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55
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1
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GATK PrintRead Producing Empty File
gatk printread written 7 days ago by BAGeno • 120 • updated 7 days ago by Pierre Lindenbaum ♦ 118k
1
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1
answer
71
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1
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ASEReadCounter More then one variant context at position
selectvariants gatk asereadcounter written 10 days ago by mb2subi • 0 • updated 10 days ago by Charles Warden ♦ 6.5k
0
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1
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108
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1
answer
Merging variant calls of whole exome and RNA-seq
snvs gatk variants rna-seq indels written 12 days ago by Saad Khan • 330 • updated 11 days ago by archie • 70
0
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114
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Remove symbolic alleles for REF in a VCF file.
vcf gatk ngs gvf baserecalibrator written 14 days ago by pmorellmi • 0
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2
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170
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2
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Removing or not removing the duplicates in .bam file
gatk picard rna-seq wgs written 21 days ago by F • 3.4k
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48
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how to run GATK CalculateGenotypePosteriors on a case-control cohort
gatk calculategenotypeposteriors written 18 days ago by blueskypie • 30
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1
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108
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1
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How treat a Bam file with mutiple read groups (RG)
gatk next-gen picard read group bam written 19 days ago by zamani_2012 • 0 • updated 19 days ago by Pierre Lindenbaum ♦ 118k
0
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60
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Mutect v1 doesnt finds second alternative allele
gatk next-gen mutect somatic written 21 days ago by guffrann • 0
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3
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2.3k
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3
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Where To Get The Annotation File For The Nimblegen Seqcap Ez Exome V1
exome gatk variant bwa written 5.9 years ago by ewre • 220 • updated 22 days ago by 477926757 • 0
1
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180
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SNP Calling Parameter Settings
vcf gatk snp written 8 weeks ago by mcclintock • 10 • updated 22 days ago by Biostar ♦♦ 20
2
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1
answer
220
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1
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VCFParseError: ploidy > 2 not supported
vcf gatk ploidy written 12 weeks ago by always_learning • 960 • updated 22 days ago by tpoterba • 40
3
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2
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127
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2
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Variant calling in large sample populations
genome gatk sequence sequencing written 24 days ago by robjohn70000 • 120 • updated 24 days ago by Pierre Lindenbaum ♦ 118k
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115
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0
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gatk4 GenomicsDBImport intervals with whole genome
gatk intervals genomicsdbimport written 4 weeks ago by Peter Chung • 80
0
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0
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98
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0
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haplotypeCaller groups comparison
gatk written 5 weeks ago by David • 150
1
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145
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0
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Difference between Private SNPs and Singleton SNPs
variant calling gatk snps snp population genetics written 5 weeks ago by prasundutta87 • 330
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1
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149
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1
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Problem installing GATK
software error gatk script ubuntu written 6 weeks ago by j.e.kelly • 0 • updated 6 weeks ago by finswimmer ♦ 11k
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77
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gatk AnalyzeCovariates The following object is masked from package stats
R analyzecovariates stats gatk written 6 weeks ago by esraesmeray1990 • 10
3
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1
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159
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1
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Can a normal tissue sequence be used for various tumor samples in Varscan Somatic or GATK MuTect2?
gatk varscan mutect2 written 9 weeks ago by tarekzakaria.badr • 30 • updated 8 weeks ago by Charles Warden ♦ 6.5k
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184
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0
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picard markduplicate output smaller file
gatk picard markduplicates bioinformatics written 9 weeks ago by Peter Chung • 80
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1
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2.3k
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10 follow
1
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Is there a easy to use GATK pipeline for SNP calling?
gatk written 11 months ago by Chen • 830 • updated 9 weeks ago by francescomusacchia • 60
3
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0
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324
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0
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ERROR MESSAGE: QD annotation at VariantRecalibrator
gatk variantrecalibrator snp written 3 months ago by Satyajeet Khare • 1.3k • updated 9 weeks ago by Biostar ♦♦ 20
2
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1
answer
382
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1
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error using bqsr and incompatible contigs
gatk bqsr written 7 months ago by cmccabe • 180 • updated 9 weeks ago by Biostar ♦♦ 20
0
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2
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193
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2
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How to combine a multi sample VCF from multiple sample VCF and interpret a multi sample vcf of bacterial genome?
vcf gatk variant calling written 9 weeks ago by S AR • 50 • updated 9 weeks ago by Pierre Lindenbaum ♦ 118k
5
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1
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147
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1
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How to merge/combine multiple vcf from different samples to make one multi sample vcf file using GATK
gatk loop scripting written 9 weeks ago by S AR • 50 • updated 9 weeks ago by Pierre Lindenbaum ♦ 118k
1
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1
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224
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1
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When to remove duplicates using deduplication in Exome-Seq
trueseq dna-seq exome-seq truseq gatk written 9 weeks ago by oriolebaltimore • 60 • updated 9 weeks ago by Charles Warden ♦ 6.5k
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