annotate_variation.pl failed for a kind of variant (INV from Pindel tool)

[kobolock]

Hi,

Annovar did not manage to pass the command (annotate_variation.pl) with this kind of variant :

chr5 176942300 176942373 ACTTTCTCAGAGCCCCAAAGCCTGTAAAACTGGCACTACCCCTACAAGTTGCAGATGATGAAACTGAGGCTCAG ATTTCTCAGAGCCCCAAAGCCTGTAAAACTGGCACTACCCCTACAAGNTGCAGATGATGAAACTGAGCCTCAGTTTCATCATCTGCAACTTGTAGGGGTAGTGCCAGTTTTACAGGCTTTGGGGCTCTGAGAAAG chr5 176942300 . ACTTTCTCAGAGCCCCAAAGCCTGTAAAACTGGCACTACCCCTACAAGTTGCAGATGATGAAACTGAGGCTCAG ATTTCTCAGAGCCCCAAAGCCTGTAAAACTGGCACTACCCCTACAAGNTGCAGATGATGAAACTGAGCCTCAGTTTCATCATCTGCAACTTGTAGGGGTAGTGCCAGTTTTACAGGCTTTGGGGCTCTGAGAAAG . PASS 0/0 . 1471 1456 15 1.01971 . . . . . INV ADN675-74 P

No result

Lets see the command below :

ANNOVAR Command: annotate_variation.pl -geneanno -buildver hg19 .../TEST_ADN675-74.VS-P.annovar .../humandb/ --splicing_threshold 50 --outfile .../TEST_ADN675-74.VS-P.annovar.variant_function ANNOVAR Started: Mon Nov 25 11:12:08 2024 NOTICE: Output files were written to ...TEST_ADN675-74.VS-P.annovar.variant_function.exonic_variant_function NOTICE: Reading gene annotation from .../humandb/hg19_refGene.txt ... Done with 72567 transcripts (including 17617 without coding sequence annotation) for 28263 unique genes NOTICE: Variants with invalid input format were written to .../TEST_ADN675-74.VS-P.annovar.variant_function.invalid_input

Please, any idea ?

Best

Sam

[kobolock]

Please, anyone could test the command please and tell me it it works for you ? Best