Bcftools extracting list of markers by chr and pos

Question

[am29]

I want to extract a list of markers from the vcf file. However, many of these markers don't have rsID, and I was wondering if is possible to extract the list of markers with bcftools using just their Chr and Pos as input?

Answer 1

[Pierre Lindenbaum]

read the manual for the option --regions-file https://samtools.github.io/bcftools/bcftools.html

The columns of the tab-delimited file can contain either positions (two-column format: CHROM, POS) or intervals (three-column format: CHROM, BEG, END), but not both. Positions are 1-based and inclusive.

[am29]

Figured it out! For anyone who might need it:

bcftools view -R CHR_BP_tab.txt file.vcf.gz > file_extracted.vcf.gz

CHR_BP_tab.txt is tab-delimited file with chromosomal and base positions, without header

[Ram]

Figured what out? Pierre showed you the exact option to use as well as how to provide the input file.