bcbio.variation.recall.vcfutils — bcbio.variation.recall 0.2.0

Utilities for manipulating VCF files

bcftools-out-type clj

(bcftools-out-type f)

duplicate-samples clj

(duplicate-samples vcf-files)

Retrieve any duplicate samples in the input VCF files.

ensure-no-dup-samples clj

(ensure-no-dup-samples vcf-files)

Ensure there are sample name duplicates in the VCF files

get-sample clj

(get-sample vcf-file)

Retrieve VCF sample name from a single sample input file.

get-samples clj

(get-samples vcf-file)

Retrieve sample names from a VCF file.

has-variants? clj

(has-variants? vcf-file)

Does a VCF file have any variants.

pog-reader clj

(pog-reader f)

Plain or gzip input reader.

region->fileext clj

(region->fileext region-orig)

(region->fileext region-orig prefix)

Convert a region to a stable file extension, handling chr1:1-100 and BED files

subset-to-sample clj

(subset-to-sample vcf-file sample out-dir)

(subset-to-sample vcf-file sample out-dir region)

Subset a VCF file, retrieving a single sample from multisample VCF. If we already have a single sample VCF, return that.