[Samtools-help] Eliminate or change filter for variant calling

[Pingilley, B. J. <ben...@my...>]

I am using the following code to do SNP variants calling.

samtools mpileup -d 50000 -f FASTA -g BAMfile | bcftools view -vcg -> VCFfile

I want to eliminate the filter which removes reads with poor mapping quality.
Also I want to be able to adjust the filter for future analysis.

How would I go about doing this?