bcftools mpileup -r flag
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!
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1 answer
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.
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