New User Advice
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GATK working, but -ERC command not found Answered0 votes 3 comments
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Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH Answered0 votes 1 comment
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Discordance genotyping Answered0 votes 1 comment
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Proper references for mutec2 working in tumour-only mode Answered0 votes 1 comment
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GATK MarkDuplicatesSpark output error Answered0 votes 3 comments
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How to provide custom exon-intron annotation source in Funcotator0 votes 4 comments
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ApplyBQSR for somatic mutation detection in HLA regions Answered0 votes 7 comments
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What should I do with vcf file now Answered0 votes 1 comment
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Where is my GATK4 ? Answered0 votes 1 comment
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Pileup output of GATK4 vs. GATK3 Answered0 votes 1 comment
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GATK GenomicsDBImport intervals Answered0 votes 19 comments
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rename sample in GVCF file Answered0 votes 3 comments
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GenotypeGVCFs produces bizarre mapping quality distribution0 votes 1 comment
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GATK Non-model organism variant call SNP site all MQ same value0 votes 1 comment
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ApplyBQSR doesn't recognise my arguments? Answered0 votes 3 comments
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Using GATK as a genotyper to genotype existing variants Answered0 votes 6 comments
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Exclude non variant sites Answered0 votes 1 comment
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GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases0 votes 4 comments
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Mutect2 somatic mutation calling for plant0 votes 2 comments
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Running best practices workflow step-by-step in command line1 vote 5 comments
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Empty intersection error when applying intervals Answered0 votes 3 comments
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GQ in jointly genotyped samples Answered0 votes 1 comment
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Script for using same GATK tool(s) on multiple sample files Answered0 votes 1 comment
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Creating dictionary for fasta reeference file Answered0 votes 1 comment
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Counld I use bam files from HISAT2 to call snp/indels? Answered0 votes 2 comments
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Help with WDL workflow for mutec2? Answered0 votes 5 comments
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Problems with FastQtoSAM Answered0 votes 3 comments