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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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make some hack job for single end reads #104

Closed Kurt-Hetrick closed 4 years ago

Kurt-Hetrick commented 4 years ago

got some bam files that had a mixture of paired end and single end reads...so yeah, will have to do something about that...might just have to do some hack job and do things somewhat manually for those couple of files.

Kurt-Hetrick commented 4 years ago

actually, i was able to implement this into the pipeline. if FASTQ_2 is null then run a single end cmd for bwa, if not, then run paired end.