Process to produce mapping quality mask

[Nilad]

Hi,

I had encounter a case with a SNP not detected by Snippy on a strain (call it 'toto'). After running Snippy-core (with "toto"), the resulting ".vcf" show for this SNP on "toto" the reference base (logical).

But why, the SNP is not detected in Snippy ?

After few try, i spot that freebayes "mapping quality" parameter is essential (-m in Freebayes). I change it of 60 (default) to 50 and the SNP is detect !

So... In my use of Snippy-core, i had already produce a bed mask of minimum coverage but, now, i am looking on a process to produce a mask on minimum mapping quality or (maybe better solution) a process to remove this SNP on the output vcf of Snippy-core.

If someone have an idea to how solve it ?

Thanks in advance for tips and help on this subject.

Have a good day =)