Non-Human
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GenomicsDBimport not importing all the batches0 votes 3 comments
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haplotypecallerspark wants DS_Store0 votes 6 comments
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Missing samples from the output vcf file produced with GenotypeGVCFs0 votes 5 comments
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emit-ref-confidence error0 votes 3 comments
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Genome STRiP - The output file of SVDiscovery is empty0 votes 4 comments
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REAL Variant not called by HaplotypeCaller0 votes 1 comment
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Error Creatting Dictionary for genome0 votes 1 comment
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MarkDuplicatesSpark not working on Putty0 votes 1 comment
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Weird log of genotypeGVCF0 votes 1 comment
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Why is GenotypeGVCF taking a long time for a smaller genome?0 votes 4 comments
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Exclude-intervals error with PathSeq0 votes 1 comment
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How do I call germline variants with multiple samples -non human?0 votes 2 comments
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FixMateInformation does not solve ERROR:MATE_NOT_FOUND1 vote 7 comments
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AnalyzeCovaiates BQSR plots on canine data0 votes 3 comments
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Disable strandbias0 votes 1 comment
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False positive Indel calling with GATK v4.1.4.00 votes 1 comment
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ApplyBQSR reduces reads quality0 votes 3 comments
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Getting an error with genomicsdbimport0 votes 9 comments
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Missing MQ scores in gvcf0 votes 7 comments
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Why does GATK haplotype caller calls SNPs from soft-clipped bases?0 votes 1 comment
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How to best use --phred-scaled-global-read-mismapping-rate0 votes 1 comment
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Access to outdated forum discussion0 votes 2 comments
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Active Region Re-assembly0 votes 1 comment
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GenotypeGVCFs stalls while using --all-sites0 votes 18 comments
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HaplotypeCaller for haploid genome0 votes 7 comments
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No individual sample info in combineGVCF0 votes 4 comments