How do I call all the variants with BCFTOOLS?

Question

[stefania.morelli92]

Hello

I am using bcftools to call variants with this command:

bcftools mpileup -B -q30 -Q30 -f reference.fasta -a FORMAT/DP,FORMAT/AD --threads 6 -R list_of_specific_position.txt file.bam | bcftools call -m  -f GQ -O v -o call_variant.vcf

For some specific variants that I am aware of (examining the bam files with Tablet), I do not get variant calls. The depth, for some, is 6 reads per site and yet they are not being called. How can I force bcftools to produce all possible variants, even if they have a low probability?

Thanks for the help

Stefania

Answer 1

[GenoMax]

Start by looking at the parameters you are using for mpileup and then for call.

 -q, --min-MQ INT        Skip alignments with mapQ smaller than INT [0]
 -Q, --min-BQ INT        Skip bases with baseQ/BAQ smaller than INT [1]

[stefania.morelli92]

Thank you for your response I'm sorry but I hadn't seen this first comment of yours I went to loosen the filters but I get the same result and it leaves me a bit puzzled!