ABRA-marked duplicates

[hr3y]

Hello,

I was wondering if anyone knows what does ABRA - Assembly Based ReAligner (https://github.com/mozack/abra) do with marked PCR duplicates?

from reading the thread I saw the recommendation to first realign and then mark duplicates (to avoid losing "hot zones" for realignment), I am actually doing 1) duplicate marking with Picard 2) realignment with ABRA

I have had good results, usually indels are found just fine, so I wonder if anyone knows if ABRA simply ignores the marked duplicates. I could not get a hold of the supplementary data in the Bioinformatics website (link simply redirects to paper), nor could I find it in the paper.

Thanks in advance!

hr3y

[mozack]

Hi,

Duplicate reads are not included in the assembly, but are eligible for realignment.

Hope that helps.