Any way to retain the ALT seq?

[rl4940]

Hi Team:

Thank you for develop this great tool
I was wondering are there any ways to retain the ALT seq, because I want to save it in the resulting consensus VCF files for transposable element calling?

I do not know about perl, but perhaps deleting some lines of your code could do this？

Thanks

[ndierckx]

Hi,

I could make this adjustment, which tools are you using for the SV calling?

[rl4940]

@ndierckx
Oh Hi and thank you for your reply!
I am using the Sniffles2, CuteSV and SVIM for combination.

Mark: Sniffles2, but not Sniffles.

Thanks for your help, and your journal was also the best benchmarking work I ve seen, really helpful!
RL

[rl4940]

The Perl really kills me hahaha^_^

[ndierckx]

I don't have my old data anymore, so could you send me those 3 vcf files, so I can test it. Will be quicker than running everything again, not into SV detection at the moment so.. You can also send to my mail nicolasdierckxsensathotmail.com

[rl4940]

@ndierckx
Thank yo so much, I am sending you in!

[ndierckx]

Sorry for the delay, forgot to put it online, version 2.3 gives the REF and ALT sequence