bcftools error: bcftools could not parse pval threshold loidly
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7 weeks 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 • 170 views
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