Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error: invalid FORMAT field, "+" #118

Open
edgarsierraorozco opened this issue Aug 29, 2020 · 0 comments
Open

Error: invalid FORMAT field, "+" #118

edgarsierraorozco opened this issue Aug 29, 2020 · 0 comments

Comments

@edgarsierraorozco
Copy link

Hello,

While trying to cal SVs from a Lumpy output, I receive this error: Error: invalid FORMAT field, "+"

Here is my code:
/Library/Python/2.7/bin/svtyper -B LA1303_int2sort.bam -i LA1303_lumpy.vcf > LA1303_svtyper.gt.vcf

And here is the header of the lumpy output:

Edgars-MBP:LA1303VCfiles edgar$ head LA1303_lumpy.vcf
SL4.0ch08 54524237 54524748 SL4.0ch08 54525091 54526259 1 0.000735835TYPE:DELETION IDS:0,5 STRANDS:+-,5 MAX:SL4.0ch08:54524248;SL4.0ch08:54526259 95:SL4.0ch08:54524248-54524335;SL4.0ch08:54525092-54526259
SL4.0ch08 51904140 51904157 SL4.0ch08 52167144 52167166 2 1.15978e-11TYPE:DELETION IDS:0,7 STRANDS:+-,7 MAX:SL4.0ch08:51904151;SL4.0ch08:52167166 95:SL4.0ch08:51904150-51904152;SL4.0ch08:52167166-52167166

Any guesses?

Thanks.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant