I have some code to pull specific SNP positions from
bcftools view , which I then annotate and apply
bcftools query, like this:
bcftools view <vcf_file>.vcf.gz Chromosome:123456 | bcftools csq -f <ref_file>.fa -g <ref_file>.gff | bcftools query -f '%POS\t%REF\t%ALT\t%BCSQ\n'
How do I give the first
bcftools view commands a list of positions in a file?
This does not work:
bcftools view <vcf_file>.vcf.gz Chromosome:<positions_file>.txt | ...etc