Represent phased blocks in VCF file

bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

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Represent phased blocks in VCF file #109

Open ramesh8v opened 3 years ago

ramesh8v commented 3 years ago

Hello, I have a mix of phased and unphased variants in the VCF file. Phased variants are represented by pipe notation "|" and the unphased variants are represented by slash notation ("/"). The phased variants are in multiple blocks/sets, they are represented by PS tag (https://samtools.github.io/hts-specs/VCFv4.2.pdf). My question is does the WASP/snp2h5 is aware of the 'PS' tag? If not, could you please suggest other ways to represent phased blocks? I'd appreciate any pointers.

Thanks, Ramesh

gmcvicker commented 3 years ago

WASP does not currently recognize the the PS tag. For now it might be best to to label all of the variants as unphased. We are in the process of upgrading the WASP pipeline and one objective is to make the phasing more flexible (using VCFs directly rather than snp2h5 conversion to hdf5), however it will likely be several months before this is available.