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Filter low-MAC variants in a VCF using bcftools (AC-based)

Source: R/filter_mac_vcf.R
filter_mac_vcf.Rd

Wrapper around bcftools view and bcftools query to:

  • keep only variants with at least one ALT allele having a minor-allele count (MAC) above a user-defined threshold, and

  • generate a blacklist of low-MAC variants.

The filter is implemented using the INFO/AC field written by the variant caller. For multi-ALT sites, the bcftools expression INFO/AC >= mac.threshold evaluates to TRUE if any ALT allele has AC >= mac.threshold. Variants that do not satisfy this condition are considered low-MAC and are blacklisted.

The function assumes that INFO/AC (and INFO/AN if present) come from a recent calling step and are still valid (i.e. no sample subsetting has occurred since calling). It does not recalculate AC/AN; it only uses the INFO fields already in the VCF.

This is a lightweight, VCF-level pre-filter that is particularly useful to slim down large, noisy VCFs (e.g. per-scaffold outputs) before merging or importing into a GDS. For GDS-level MAC filtering based on genotypes, see filter_ma.

Filter target: VCF variants.

Usage

filter_mac_vcf(
  vcf,
  mac.threshold = 4L,
  out.vcf = NULL,
  blacklist.file = NULL,
  bcftools.path = "bcftools",
  compress = TRUE,
  index = TRUE,
  verbose = TRUE
)

Arguments

vcf

(character) Path to the input VCF (.vcf or .vcf.gz).

mac.threshold

(integer) Minimum ALT allele count required to keep a variant. Variants where all ALT alleles have AC < mac.threshold are removed. Default: mac.threshold = 4L.

out.vcf

(optional, character) Output VCF filename for MAC-filtered variants. If NULL, the function generates a filename from the input VCF root by appending ".mac.vcf" and ".gz" when compress = TRUE. Default: out.vcf = NULL.

blacklist.file

(optional, character) Path to a TSV file storing low-MAC variants (CHROM, POS, ID). If NULL, the function generates a filename from the VCF root by appending ".mac_blacklist.tsv". Default: blacklist.file = NULL.

bcftools.path

(character) Path or name of the bcftools executable (e.g. "bcftools" or a full path inside a conda environment). Default: bcftools.path = "bcftools".

compress

(logical) Compress the output VCF using bgzip (-Oz). Default: compress = TRUE.

index

(logical) Index the output VCF with tabix when compress = TRUE. Default: index = TRUE.

verbose

(logical) Show progress messages and bcftools command lines. Default: verbose = TRUE.

Value

Invisibly returns a list with:

  • mac.vcf – path to the MAC-filtered VCF;

  • blacklist – path to the low-MAC variant list;

  • log – path to the bcftools log file.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
filter_mac_vcf(
  vcf            = "chr1_freebayes_poly.vcf.gz",
  mac.threshold  = 4L,
  out.vcf        = NULL,   # will append ".mac.vcf.gz" by default
  blacklist.file = NULL,
  bcftools.path  = "bcftools"
)
} # }