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? # for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? # 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: