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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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germline calling from multiple chromosomes #7

Open twoneu opened 1 year ago

twoneu commented 1 year ago

Hello all,

Thank you for making this great tool. In the example, the germline caller is used for chromosome 20 only. If we wish to perform germline calling for chromosomes 1-22 for a single sample, do we need to run the germline caller 22 times? Or is there a way to input multiple fasta files that correspond to the different chrs?

jinzhuangdou commented 1 year ago

There is an option --region in which you can specify multiple chromosomes. You can set region.lst as following to run 22 chromosomes at the same time.

region.lst chr1 chr2 chr3 ... chr22

monoplasty commented 12 months ago

Hello,jinzhuangdou

 -g REFERENCE, --reference REFERENCE
                        The human genome reference used for alignment

When I set the region.lst content to chr1-22, how do I specify the reference?