all vcf records annotated as `INS:ME:SVA`when using a custom library

[jazberna1]

Hello @simoncchu,

I managed tu run xTEA with a custom mouse library for which you guided me here in this ticket:
#139

I have obtained the following vcf file as output (attached as aligned.sorted.marked_duplicates_SVA.vcf.txt):

aligned.sorted.marked_duplicates_SVA.vcf.txt

What I have noticed is that in the vcf all the events are annotated as INS:ME:SVA even though in my custom gnrt_pipeline_local_v38.py script I am not looking for SVA in the for s_rep_type in l_rep_type loop of the script that iterates through the ME types.

This is my custom gnrt_pipeline_local_v38.py script (attached as gnrt_pipeline_local_v38.py.txt)

gnrt_pipeline_local_v38.py.txt

I was wondering if the code that creates the vcf just annotates all the records as SVA as a side effect of me providing a custom library in which case this would be a problem since I know the specific ME type that is contained in the library.

Many thanks for your help.
Jorge

[simoncchu]

Hi @jazberna1, thank you for reporting this. It's a bug that need to be fixed. Mainly because not sure what type of TE it is when in a customized mode, and it goes to "else" branch which gives a type of "SVA". It will not affect the results, but only the annotation. I'll change to a different term in the next release.