search

wdecoster / surpyvor

A python wrapper around SURVIVOR
MIT License
19 stars 1 forks source link

query on surpyvor prf #20

Open prasundutta87 opened 3 years ago

prasundutta87 commented 3 years ago

Hi,

I was trying to use both surpyvor and truvari for SV benchmarking. Truvari has an option to input a bed file to limit comparison to only high confidence bed regions. Is it possible to have that feature in surpyvor as well? I am aware that the same can be achieved by using bedtools on both test and truth VCFs and then run surpyvor on them, but this feature in surpyvor can be helpful for such a purpose.

Regards, Prasun

wdecoster commented 3 years ago

Hi Prasun,

Thanks for your suggestion. That is currently not implemented, but it shouldn't be too hard to add that in the future. I can't make any promises though.

Regards, Wouter

prasundutta87 commented 3 years ago

Thanks a lot @wdecoster ! Just wondering if you had the chance of comparing the results between Truvari and surpyvor prf when you were developing the later.

wdecoster commented 3 years ago

No, I did not look into that.

prasundutta87 commented 3 years ago

Just an additional request, can the --plotout option can be added in the prf program as well please so that the venn/matrix /bar plots can be given their specific names instead of venn.png, bar.png, etc.? It overwrites the existing files in case you don't run the program in different folders. I have hard-coded a workaround for this issue in my script as of now.

wdecoster commented 3 years ago

Oh yes that would be good too