As was talked about in issue #340, given an incorrectly formed ref/alt allele combo of GT/C, oncotator adjusts this to CT/C. This does not follow with what is in the reference genome. I would suggest either a more thorough validation of these indels.
Note: The example VCF that brought about this issue originated from the TorrentSuite software, which is what some IonTorrent users utilize for variant calling.
As was talked about in issue #340, given an incorrectly formed ref/alt allele combo of GT/C, oncotator adjusts this to CT/C. This does not follow with what is in the reference genome. I would suggest either a more thorough validation of these indels.
Note: The example VCF that brought about this issue originated from the TorrentSuite software, which is what some IonTorrent users utilize for variant calling.