Exome sequencing quality filtering

[Kath]

Hi,

I am using exome sequencing data to call variants in patient samples and would like to know what quality control is generally applied before mapping. At the moment I am using fastx_quality_filter to filter out reads with <80% at <q30. Is this too stringent?

Thanks

Kath

[Bukowski]

It depends what your downstream tools are. Some are quality aware, some can recalibrate base quality scores after alignment. Personally I do not quality filter my reads prior to alignment for quality, especially not a read level quality metric. If you're going to do anything, just trim low quality bases at the ends of the reads, it's most likely that this is the part of the read most likely to suffer.