Lauren Fedenia
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DP for each variant bulk is skewed towards 50 and multiples of 50
When using the GATK pipeline to call variants, I end up obtaining a DP for each variant skewed towards 50 and multiples of 50 (see photo below) when my average read depth from my sequencing files ...
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Paired-End Reads and Variant Calling
I am trying to call variants from paired-read whole genome reseq data. I have two fastq files (forward and reverse) for each sample. I got to the MergeBamAlignment command and no matter what I tr...
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How do I input two separate paired-end fastq files into the GATK pipeline? Do I use an interleave-fastq?
AnsweredCan you please provide a) GATK version used 4.0.3.0 b) Exact GATK commands used c) The entire error log if applicable.