Filter, deduplicate, and check an annotated indel VCF

Helper used by annot_vcf_to_83_catalog, annot_vcf_to_89_catalog, and annot_vcf_to_476_catalog to perform shared preprocessing: rename #CHROM to CHROM, optionally filter to PASS variants, warn about positions with differing ALT alleles, and deduplicate by position.

Usage

quick_check_vcf(annot_vcf, FILTER_PASS = FALSE, do_message = FALSE)

Arguments

annot_vcf

A data frame with at least columns CHROM (or #CHROM), POS, and ALT. If FILTER_PASS is TRUE, a FILTER column is also required.

FILTER_PASS

If TRUE, retain only rows where the FILTER column equals "PASS".

do_message

If TRUE, emit diagnostic messages showing row counts at each processing step.

Value

A data frame deduplicated by position, with a pos_id column added.