Does phase_common use phase sets in WGS-derived VCF files?

odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool

https://odelaneau.github.io/shapeit5/

MIT License

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Does phase_common use phase sets in WGS-derived VCF files? #39

Closed fwplace closed 1 year ago

fwplace commented 1 year ago

Hello, Thank you for providing this wonderful tool. I am currently working with VCF files that have phased genotypes on certain variant sites when they are close. The majority of variants in the VCF files are unphased, while only a small portion are phased by GATK. I have noticed that shapeit4 can utilize the phase sets from the PS field in VCF files. Since phase_common has replaced shapeit4, I am wondering if it can also make use of this phasing set information.

odelaneau commented 1 year ago

Sorry about this. It's one of the functionality I have not yet moved to S5 and tested. If you want to use PS, please use S4. Thanks.