Use bcftools to call variants
To generate variant calls in the VCF format, run bcftools mpileup, followed by bcftools call:
where:
-Ob: we want the output to be a BCF file (i.e. binary VCF). To output a text VCF, use -Ov.-m: use the default variant calling method-v: only output the variants (i.e. don’t list the sites where we match the reference sequence)We preloaded your sandbox with the variable $REF_FASTA. You can use the command to list variables and echo to view their value, e.g. .
Then to view the variants, run:
See the official bcftools guide to variant calling for more details and variations on this process.