bcftools error: bcftools could not parse pval threshold loidly
0
0
Entering edit mode
14 months ago
mut.patricia ▴ 20

Hi, I want to call variants with bcftools mpileup + call for human Y chromosome, but I got the error "Could not parse: --pval-threshold loidy" The code I am using:

bcftools mpileup -f refY.fa -d 2000 -q 30 file.bam | bcftools call -m -V indels -ploidy 1 -Ov -o calls.vcf

It generates a vcf file with variants though. Does what does anyone know what the error means? Did not find it googling.

Thanks! Patricia

bcftools mpileup • 387 views
ADD COMMENT

Login before adding your answer.

Traffic: 1964 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