what mean samples are phased

Question

[sami]

I would like to know what mean samples are phased in bcftools? Bcftools:

-p/P, --phased/--exclude-phased select/exclude sites where all samples are phased

Thank you

Answer 1

[Ram]

You should search online for a more robust definition, but phasing samples refers to determining which allele comes from the mother and which comes from the father. Unphased genotypes are usually notated in the format x/y, where x and y are the two genotypes (like 0/1 or 0/0 or 1/1). Phased genotypes use the | symbol: x|y or y|x (example: 0|0, 1|1, 0|1), depending on which parent each allele comes from. IIRC, Phasing always puts maternal allele in the front followed by the paternal allele : mat_allele|pat_allele.