2 hours ago by
Hi,
I am using bcftools filter. I run bcftools filter command in two different ways. It gave me different results.
Command #1
bcftools filter --e "GQ<20" miss.GT.vcf.gz>test1.vcf
This gave me 49336 variants.
while when I run command 2
bcftools filter -i "GQ>20" miss.GT.vcf.gz>test2.vcf
It gave me 80858 variants.
There are 80858 variants in original file.
Why there is such variation? Which command results should I consider for further analysis?
