Variant Calling with Bcftools Call instead of Bcftools View

Variant Calling with Bcftools Call instead of Bcftools View

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I’m revisiting variant calling from when I used an older version of bcftools, but found the newer sam/bcftools have deprecated some commands and parameters. This led me to retaining what I feel are too many loci (100’s of thousands vs. 10’s of thousands).

In previous versions, I was running something like:

bcftools view -c -g -d 0.8 -p 0.01 -P full -t 0.001 -v foobar.bcf > foobar.vcf

But am now running:

bcftools call -m -v -p 0.01 -P 0.001 -O v foobar.bcf > foobar.vcf

I switched to the recommended multiallelic caller though consensus caller is still functional. I suspect so many loci are retained because I’m not skipping them where less than some fraction of samples are covered (the -d parameter has been removed; fraction was 0.8 in this case). Is there another approach to this, or should I try to use an older version?

It also seems like they switched the substitution rate from parameter -t to -P, and got rid of the original -P for specifying a full prior. They also removed the -g parameter for calling genotypes at variant sites, though I’m guessing this is done by default when outputting variants only with -v ? Please correct me if I’m wrong here.

Any help is much appreciated!


mpileup


samtools


bcftools


variant-calling

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