Description
The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.
Input
Optional ploidy definition file for the fixploidy plugin (-p), with
space/tab-delimited columns: CHROM, FROM, TO, SEX, PLOIDY.
e.g. 'ploidy.txt'
Optional sample sex assignment file for the fixploidy plugin (-s),
containing lines of the form: NAME SEX.
Samples not listed are treated as female by the plugin.
e.g. 'samples_sex.txt'
Optionally restrict the operation to regions listed in this file (indexed input required; passed as a bcftools regions file argument). e.g. 'regions.bed'
Tools
bcftools Documentation
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools plugin fixploidy Documentation
Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.
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