Entering edit mode
9.0 years ago
nuketbilgen
▴
40
Hi,
I am new in the next generation analysis. I have 3 whole gene sequences.
I have several questions,
- How should I decide mapQuality filter value? Most of my reads has 60, but when I use 60 to filter my reads I lose approximately 3kb in one gene.
- Is it possible to give different MapQ values for different chromosome with bamtools? I am planning to use in one gene mapQuality">=20" and in the other two genes mapQuality">=60".
Thank you
What do you want to do? There's often no need to explicitly filter by MAPQ.
Hi,
I want to generate a gvcf file (I have a pipeline ready for that). But when I use with mapQuality 60 filter I lose approximately 50 variation.
After I get the gvcf file, haplotype determination in individual level and population level. I am working with cows :)
Thank you
Fristly, 60 is an absurdly high quality to use for filtering, maybe 10 or so would be more useful (afterall, a MAPQ of 60 would bias against finding real variants, since any alignment showing a variant is more likely to have a lower MAPQ score). Secondly, some variant callers (e.g., GATK UnifiedGenotyper and samtools mpileup) will perform some filtering for you anyway.