Missing chromosome information in annotated file

Open adthrasher opened this issue 5 years ago • 1 comments

This may only be an issue with hg38, but it is possible for the annotated output file to have a record with no chromosome information for one of the partners, which causes sv_inframe.pl to fail.

SJLGG064626_D1 GTPBP4 chr10 992606 + coding - > 4 85 0.00 0.00 118 0.07 0.01 86 137 79 0 CGAAAGACTCCAACCGTTATTCATAAACATTACCAAATACATCGCATTAGACATTTTTACATGAGAAAAGTCAAATTTACTCAACGAAAGACTCCAACCGTTATTCATAAACATTACCAAATACATCGCATTAGAC CTX

Feb 03 '20 16:02 adthrasher

Another example:

SJLGG064626_D1 - CBWD5_locC,CBWD3 chr9 68232051 + intron > 5 127 0.00 0.80 213 0.01 0.05 134 0 25 GTCCTGGCTGAGGAGTGGTTCCAGCAAAGTGGACTCTTCCACGTCCTGCAGCTCCCCCAGTGGCGCCGGATCTAGGAAATATTGTGCCTTTTGCTGAAACTCTGGGGTTGACAGGAGCTCATCTAACAGGCTGGAGGCCCATAGGTGGAAGGGACTTGCCTTGTCTCGGATGAGACTTTGGACTTTGGACTGTGGACTTTTGAGTTAACACTGAAATGAATTAATGCTGAAATGAATTAAGACTTTGGGAGACGGTTGAGA CTX

Feb 03 '20 17:02 adthrasher