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RemoveNearbyIndels: CRSP0 votes 6 comments
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HaplotypeCaller on multiple BAMs vs Joint-Call Cohort0 votes 3 comments
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Output vcf file from HaplotypeCaller mostlly contain <NON_REF> alteration0 votes 3 comments
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Can't add to PATH0 votes 2 comments
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Equations in AS_StrandOddsRatio aren't shown correctly0 votes 1 comment
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Error with GATK 4 and R gsalib0 votes 2 comments
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ERROR while calling variants...0 votes 2 comments
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Character cannot be cast to java.lang.Integer Exception0 votes 1 comment
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Picard CollectHsMetrics PCT_EXC_OFF_TARGET1 vote 4 comments
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Paired-End Reads and Variant Calling0 votes 1 comment
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ReciprocalOverlapAnnotator error for Sniffles data0 votes 2 comments
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Problem Installing and testing GATK-4.1.7.01 vote 5 comments
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A USER ERROR has occurred: Number of read groups must be >= 1, but is 00 votes 4 comments
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Do I need to perform fastqc and adapters trimming before gatk pipeline?1 vote 4 comments
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Read Group: ID for split files of multiple samples on multiple lanes0 votes 7 comments
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Workaround for Missing Platform Identifier in BQSRPipelineSpark?0 votes 1 comment
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Posts pending approval now for 1 month0 votes 1 comment
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Unable to replicate the spanning deletions documentation0 votes 8 comments
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How to set a COMPRESSION_LEVEL of ApplyBQSR0 votes 6 comments
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Error while running HaplotypeCaller with gatk 40 votes 1 comment
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Broken: conda env create -n gatk -f gatkcondaenv.yml0 votes 15 comments
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Trouble Installing GTAK0 votes 2 comments
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I have no idea why error occurs...(also used java8)0 votes 1 comment
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gatk4-output from baserecalibrator and apply BQSR0 votes 1 comment
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ValidateSamFile tmp not found ERROR with not output or Exception0 votes 4 comments
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Typo in VQSR tutorial0 votes 1 comment