New User Advice
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Splitting a final filtered VCF file based on sample list and MAF Impact1 vote 2 comments
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GATK MarkDuplicates Missing output file1 vote 5 comments
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Scatter Gather principle by chromosome on Gatk1 vote 2 comments
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Proper way to prepare .bam for MarkDuplicatesSpark Answered1 vote 3 comments
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Running best practices workflow step-by-step in command line1 vote 5 comments
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Unable to unzip GATK0 votes 4 comments
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Collecting alignment metrics at READ_GROUP level with Picard0 votes 4 comments
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GATK Installation MS windows 110 votes 1 comment
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Using CrosscheckFingerprints (Picard) on mice RNAseq data0 votes 1 comment
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GATK Germline CNV calling0 votes 8 comments
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Tumor-match mode doubt0 votes 1 comment
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Comprehending Duplicates in Mutect2 and filtering0 votes 2 comments
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Base Quality Score Recalibration doubt0 votes 4 comments
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Tumour Match Mutect0 votes 1 comment
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Creating PON0 votes 2 comments
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Germline Variants Calling0 votes 5 comments
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gatk4.5 markduplicatesspark error spark0 votes 4 comments
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VariantFiltration isn't working0 votes 1 comment
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GenomiCDBImport issue0 votes 9 comments
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Checking of GATK script0 votes 1 comment
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GATG-4.80 votes 1 comment
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Contig names lost after FastaAlternateReferenceMaker0 votes 4 comments
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BQSR error0 votes 4 comments
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Joint Call on individuals sequenced with differing coverage0 votes 2 comments