bcftools mpileup -r flag

Question

[sarah.goldstein]

Help!

I am trying to use bcftools mpileup to call variants on a set of 13 genomes. I have a reference genome that is assembled into 9 contigs. I am only interested in the SNPs on contig 2. How exactly can I use the -r flag to specify that I only want to look at contig 2?

Looking at tutorials some have regions specifies as follows:

samtools mpileup -uD -r 2L:100,000-150,000

What does the 2L mean here? I understand the 100,000 - 150,000 indicates searching for the 50KB region.

Thanks!

Answer 1

[microfuge]

2L should mean the chromosome/contig name. Needs to be substituted with the contig name where you want to call SNPS. I think that omitting the coordinates would do the analysis for the entire chromosome/contig.