New User Advice
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Scatter Gather principle by chromosome on Gatk0 votes 1 comment
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Where can I download Homo_sapiens_assembly38.haplotype_database.txt0 votes 2 comments
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Unclear why Picard ValidateSamFile is producing an error Answered0 votes 6 comments
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CollectSamErrorMetrics error Answered0 votes 3 comments
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no gatk installation0 votes 0 comments
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VariantFiltration issue Answered0 votes 3 comments
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Find rate of homozygosity Answered0 votes 4 comments
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GenomicsDB Import issues0 votes 1 comment
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Package ‘gsalib’ was removed from the CRAN repository. Answered0 votes 3 comments
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Proper way to prepare .bam for MarkDuplicatesSpark Answered1 vote 3 comments
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A USER ERROR has occurred: Contig chr1_KI270762v1_alt not present in reads sequence dictionary Answered0 votes 5 comments
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GenomicsDBImport - why "intervals" is required?? Answered0 votes 3 comments
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Gatk4 rnaseq germline snps indels json file Answered0 votes 3 comments
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Variant Quality Score Recalibration Answered0 votes 3 comments
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How to use WGA Data in picard Answered0 votes 3 comments
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Suggestions to find pathogenic variant Answered0 votes 4 comments
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Error, ShouldNeverReachHereException, FuncotationMap in FilterFuncotations Answered0 votes 20 comments
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GATK working, but -ERC command not found Answered0 votes 3 comments
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Somatic mutation detection in HLA regions using hg38 alt-aware alignments Answered0 votes 2 comments
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ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu Answered0 votes 13 comments
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Proper references for mutec2 working in tumour-only mode Answered0 votes 1 comment
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Estimate genotype proportions from filtered variants0 votes 5 comments
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Discordance genotyping Answered0 votes 1 comment
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Picard CrosscheckFingerprints not identifying samples from the same individual as a MATCH 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