error when using shapeit2 phasing with vcf from GATK
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4.2 years ago

my command line: shapeit.v2.r837.GLIBCv2.12.Linux.static/bin/shapeit --input-map /genetic_map_b37/genetic_map_chr3_combined_b37.txt --input-vcf filtered.vcf --output-max shapeit_phasing.chr3.phased

and I got the error: ERROR: Site pos=15274 alt=G,T is not bi-allelic!

I can't find any answer anywhere. 1. shapeit could accept vcf file, but it doesn't say what kind of vcf it can handle. 2. I tried to use GATK VariantsToBinaryPed to transform the vcf file, but I don't have the metaData(.fam) file since I only have one sample.

I'm sorry that I'm new in phasing. Can anybody give me hand? THANKS!

vcf shapeit phasing • 1.7k views

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