germline calling from multiple chromosomes

[twoneu]

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]

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]

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?

[Arsenalwins]

Hi! I have same question with @monoplasty, I want to see all the somatic SNV in the genome of my sample. Should I repare the 23 .fa one by one or just one fa for the whole genome? I think this kinds of appliction of the technique is in great need, more specific illustration will benefit us a lot @jinzhuangdou.