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Old 04-30-2020, 03:02 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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It may be best to use "mutate.sh" (to look at in-line help) to introduce the mutations after you generate the reads with randomreads.sh. You will get a VCF files of changes.

I think using "local=t" is causing the alignment issues. It is meant for local alignments when you expect errors at end of reads.

Last edited by GenoMax; 04-30-2020 at 05:49 AM.
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