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How to get individual strand counts from Mutect2 for multi-allelic sites
gatk4 vcf mutect2 written 7 months ago by nickeener20 • updated 5 months ago by Biostar ♦♦ 20
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Filtering for individual allelic balance in multisample vcf using GATK4
vcf gatk gatk4 filtering written 5 months ago by mernster0 • updated 5 months ago by chrchang5236.7k
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GATK4 (4.1.2.0) Mutect2 --germline-resource option
gatk4 mutect2 written 5 months ago by romagnoli.simone0 • updated 5 months ago by RamRS26k
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Temporary Directory Problem in GATK4
gatk4 directory java temporary written 19 months ago by BAGeno170 • updated 7 months ago by jerome.irianto0
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Tranche Plot after VSQR
gatk4 variantreclibration written 7 months ago by BAGeno170 • updated 7 months ago by Nicolas Rosewick8.7k
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Suggest vcf filtered parameter for gatk VariantFiltration
gatk4 snps written 10 months ago by Mbillah110 • updated 10 months ago by WouterDeCoster43k
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VQSR with extremely low TPs (<0.01), How low can tranche goes?
exome vqsr gatk4 snp written 12 months ago by greyman80 • updated 12 months ago by ATpoint32k
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A strange problem with annotation of vcf file
genome annotation vcf bcftools gatk4 written 19 months ago by seta1.2k • updated 15 months ago by zx87549.1k
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GATK best practices for Broad-produced NGS data
gatk4 ngs broadinstitute variantcalling written 16 months ago by Mehulsharma.25310 • updated 16 months ago by vdauwera960
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Stop GATK MergeBamAlignment from unmapping reads
gatk4 gatk alignment bam mergebamalignment written 16 months ago by ttmigueltt10 • updated 16 months ago by finswimmer13k
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Combining snp and indel vcf files with GATK4
gatk4 varint calling combin variant sortvcf written 18 months ago by seta1.2k • updated 18 months ago by harold.smith.tarheel4.5k
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GATK4 training for beginners
gatk4 training written 2.2 years ago by emmanouil.a20 • updated 2.0 years ago by vdauwera960
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Using gVCF mode in HaplotypeCaller ( GATK4)
gatk4 haplotypecaller snp written 2.2 years ago by ahmad mousavi470 • updated 2.2 years ago by JJ500
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News: Deep learning in GATK4
gatk4 gatk news deep learning written 2.3 years ago by vdauwera960
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Forum: Are you using GATK ?
gatk4 gatk forum written 2.4 years ago by tiffanym20
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