Variants That Fall Within Pseudogenes

Question

[Rajendra Bahadur Shahi]

Any idea, removing variants that fall within pseudo-genes in exome analysis

Answer 1

[Sean Davis]

Mapping quality is potentially useful for doing so. In particular, even a few reads with low to zero mapping quality can be indicative of a problematic region. Along the same lines, mappability (available at UCSC) is often reduced in regions with false positive variants. Note that not all regions that are problematic are pseudogenes.

[Sean Davis]

And the extent to which the regions are problematic will depend on the analytical tools used, including the aligner, post-processing of BAM files, and the variant calling strategy.

Answer 2

[Irsan]

Use a smart genotype caller like GATK's HaplotypeCaller and it will deal with this problem and many other false positive variants.