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
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
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