Entering edit mode
2.0 years ago
yoser4
▴
10
Hello everyone
I have a vcf file (snp) of 99 samples, after filtering with vcftools, the code is as follows:
vcftools --gzvcf my.vcf.gz \
--maf 0.05 \
--max-missing 0.8 \
--recode \
--out /group/zhougrp3/zhangyuan/haoli/sheep99_wgs_snp/99WGS_snp/filtered_output
A problem occurs: There seems to be a problem with a GT, as follows:
The first picture above is the original vcf file, and the second one is the filtered vcf file. I used a shell script to change the delimiter to make the difference more intuitive (the shell doesn't change the result, it's just easier to see).
As we can see, there is a GT here, transformed from the original .|.
to .
I would like to ask:
- Why does such a problem occur? Is my filter code used incorrectly?
- I want to use beagle to fill the filtered results. The
"."
in this place will have an error:ERROR: Missing one or both alleles for a genotype
, how can I solve this error?
Any reply will be greatly appreciated
Thanks a million