Question: Variants That Fall Within Pseudogenes
gravatar for Rajendra Bahadur Shahi
6.9 years ago by

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

snp pseudogene • 2.1k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 6.9 years ago by Rajendra Bahadur Shahi0
gravatar for Sean Davis
6.9 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Sean Davis26k

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.

ADD REPLYlink written 6.9 years ago by Sean Davis26k
gravatar for Irsan
6.9 years ago by
Irsan7.2k wrote:

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

ADD COMMENTlink written 6.9 years ago by Irsan7.2k
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