Other
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Liftover Picard hg19 to hg38: variants were not successfully lifted over2 votes 2 comments
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Do I need to perform fastqc and adapters trimming before gatk pipeline?2 votes 4 comments
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Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH2 votes 2 comments
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Any automatic downloadable gatk3?2 votes 13 comments
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GenomeSTRiP SVPreprocess error1 vote 1 comment
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HaplotypeCaller -ERC GVCF -variant_index_type LINEAR1 vote 1 comment
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How do I rename output folder created using glob (WDL-Cromwell)?1 vote 1 comment
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GenomicsDBImport: has too many genotypes in the combined VCF record1 vote 2 comments
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Merge different individual VCF1 vote 11 comments
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Picard CollectHsMetrics PCT_EXC_OFF_TARGET1 vote 4 comments
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Problem Installing and testing GATK-4.1.7.01 vote 5 comments
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jar for mutect 1.1.71 vote 6 comments
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GATK/Picard does not detect mates in paired-end BAM1 vote 3 comments
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HaplotypeCaller produces very large .idx files1 vote 4 comments
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ValidateSamFile behavior1 vote 7 comments
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Problem Installing GATK python environment - SOLUTION POSTED! Featured1 vote 17 comments
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Typos in docs1 vote 1 comment
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MarkDuplicatesSpark crash1 vote 10 comments
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FastaAlternateReferenceMaker generates same sequence for multisample vcf0 votes 0 comments
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GATK ContaminationModel0 votes 0 comments
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Error while running HaplotypeCaller0 votes 1 comment
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Picard LiftOver behaviour for multiallelic positions0 votes 1 comment
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ASEReadCounter does not return the value only for chrX0 votes 2 comments
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HaplotypeCaller confuses introns as long deletions0 votes 3 comments
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error when running ASEReadCounter0 votes 2 comments
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SortSam - Question about I/O error0 votes 2 comments