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Hi,
I'm attempting to run the tool on a specific chromosome using the --chroms arg. My command looks like such:
python //file.bam //file.fa //output-prefix --loci //file.bed --chroms 19 --debug --trf_args 2 7 7 80 10 50 500
I've tried running this both with "--chroms 19" and "--chroms chr19," but either way, the scan seems to start at chr1, which seems like a waste of resources. Please advise. Thanks for making this!
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