We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
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
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.
The text was updated successfully, but these errors were encountered:
No branches or pull requests
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.
The text was updated successfully, but these errors were encountered: