How to convert Haps file to vcf file?
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7 months ago
SeoG • 0

I got the haps file and sample file after pre-phasing with eagle2. After that, I tried to switch to a vcf file using SHAPEIT4, but it keeps saying that there is no index file. How can I easily convert to a vcf file? Thank you

pre-phasing GWAS imputation • 389 views
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unzip haps then:

   bin/shapeit \
    -convert \
    --input-haps {haps_prefix} \
    --thread {cpus} \
    --output-vcf {phased_vcf};
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