adamewing/bamsurgeon

DEL not considering VAF Input

Opened this issue · 5 comments

jelisavetailic commented

Hi,

I have created an input for addSV in which there are deletions with different VAFs (0.6, 0.9 etc.). However, in the final VCF all DEL are with VAF 1 meaning that all reads are deleted. Could you elaborate a bit more on how BamSurgeon insert deletions, and how to make it insert DEL with VAF 0.6?

Thank you.

adamewing commented

Sure - could you let me know which version you're using (I'd recommend the latest commit on github) and an example of a deletion from your mutation input file?

jelisavetailic commented

Hi,

These are the test examples:

1.
input mutations:
chr1 205272063 205297375 DUP 5
chr2 47333665 47337771 DEL 0.6

output VCF:
first_ex

2.
input mutations:
chr1 205291301 205296266 DUP 3 0.6555650690707391
chr2 47336616 47337032 DEL 1 0.05978037007937531

output VCF:
second_ex

3.
input mutations:
chr1 205291301 205296266 DUP 5
chr2 47336616 47337032 DEL 0

output VCF:
third_ex

As you can see all VAFs in output files are 1.0. My goal is to find a way to calculate the number of DUPs (copy numbers) and VAF of deletions in the output file. If I have DUP 5 in input file, how can I find that information in the output file (except visually inspecting in BAM Viewer).

As for the version, it is 1.0.

Thanks!

jelisavetailic commented

I have updated the version to 1.2, however, everything remains the same.

adamewing commented

Apologies for the delayed response and apologies for not being clear: I meant grab the latest commit rather than the latest tagged verson which was quite outdated. I've just updated the latest commit to be version "1.3" - since "1.2" there have been quite a few bugfixes including changes to the VCF output so there's a chance the VAF in the VCF output has been corrected (hope so anyway). If it's still reporting VAF=1.0 for everything let me know and hopefully it's an easy fix (will test on my end as well).

jelisavetailic commented

Hi, thank you for the reply. I did take the latest commit (with python3), and not latest release, I have mistaken in the last reply. And I am still getting VAF 1.0. anyways. In the final BAM final it is indeed 1.0, and I would like it to be the number I put in VCF. Thank you! Is there maybe some other possibility why it is ignoring the VAF given?