How to get unphased VCF file phased by shapeit?

I have a vcf file at hand and tried to get it phased by shapeit.

The command line was referred here.

like this:

shapeit --input-vcf gwas.vcf \
         -M genetic_map.txt \
         -O gwas.phased

The result were

ERROR: No GT found at site idx=0 pos=0

Who knows what was wrong?

Thank you for help!

sequencing software-error genome

• 4,085 views • link

updated 4.5 years ago by Ram

• written 11.7 years ago by Jie Ping •

0 answers

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