error when using shapeit2 phasing with vcf from GATK
0
0
Entering edit mode
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
ADD COMMENT

Login before adding your answer.

Traffic: 3026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6