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Missing chromosome information in annotated file #9

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adthrasher opened this issue Feb 3, 2020 · 1 comment
Open

Missing chromosome information in annotated file #9

adthrasher opened this issue Feb 3, 2020 · 1 comment
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@adthrasher
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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
@adthrasher
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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

@adthrasher adthrasher added the bug Something isn't working label Jun 12, 2020
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@adthrasher