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.
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.