Do you have any recommended standard filter? about ervcaller HOT 4 CLOSED

According to feedback from users, researchers have different filtering standards.
It did indicate type 0 is less confident according to supporting reads, although i will not suggest to directly filter them out.
chr and position did indicate the breakpoints as most tools does. the START & END you highlighted below are the information on the inserted TEs but not human coordinates.
As the example showed, the predicated HERV's insertion position will be chr1:5617379.

I will suggest to filter low quality TE genotypes, such as GQ>20 or others; check if a called TE insertions located within same type of reference TE; filter by total depth of supporting reads (DPI) according to your depth; filter out TEs with extremely long TSD, which is rare but may still real, unless you want to analyze this group.

Xun

from ervcaller.

thanks,
I have other questions, I didn't find gatk process, like markduplicates, realign, recalibration, on your paper.
why didn't use it?

from ervcaller.

Thanks for your suggestions.

We want to make ERVcaller easy to install and use. We did consider to include QC steps, although they can be preprocessed by many other tools. And we also assumed most users would already perform read QC separately, such as removing redundant reads, low-quality reads, adaptor sequences etc. thanks again, we may reconsider to include those steps in our next version.

We performed a realignment process as well in ERVcaller, which may be slightly different with GATK.

We did not have the recalibration process because it is for evaluating quality scores for SNPs, InDels but not for TE insertions as I know.

Thanks,
Xun

from ervcaller.

Thanks for perfect answer.

from ervcaller.