How do I call all the variants with BCFTOOLS?

[More92]

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

[pd3]

You can check the output of the mpileup step to see if your read filtering is not too strict, the AD tag shows the number of reads that were included in the calling. Then the genotype likelihoods (PL) is used to at the call step to determine the genotype, the sensitivity there can be increased with the -P option. It is also a good idea to check visually in IGV what the data looks like.