Hi, I was calling SNPs with bcftools pipeline as below:

bcftools mpileup --threads 20 -a AD,DP,SP -Ou -f ${REF} ${BAM}/*.bam | bcftools call --threads 20 -f GQ,GP -mO z -o ./output.vcf.gz

But the option --threads didn't work and this calling has taken about two weeks to output a 71G vcf file.

According to the instruction of bcftools only work for compression of output file when the output type is b or z. I've changed the output type to -Ob, but multiple threads still didn't work either.

So, how can I speed up this calling process?

Thank you