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Published 20 hours ago • verified publisher icon hall-lab

Error: invalid FORMAT field, "+"

Open edgarsierraorozco opened this issue 3 years ago • 0 comments

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.

edgarsierraorozco avatar Aug 29 '20 18:08 edgarsierraorozco