bcftools isec question?

Question

[vctrm67]

How does bcftools isec work, ie. which parameters does it intersect on? I was assuming chromosome, position, ref, and alt alleles only, and disregards any information in the INFO, FILTER, etc. columns. Or does it intersect on any other fields in the VCF?

Answer 1

[Pierre Lindenbaum]

http://samtools.github.io/bcftools/bcftools.html#common_options

-c, --collapse snps|indels|both|all|some|none|id

Controls how to treat records with duplicate positions and defines compatible records across multiple input