If there are common prefix being removed, or end position is altered (when end position is missing or is not correct), start position and / or end position might be updated. We have a new field in genome nexus response, e.g. "genomicLocationExplanation":"End position changes from 123 to 122, because end position should be the position of last deleted nucleotide.
Add comments for failing variants, we have a new field called errorMessage, e.g. "errorMessage": "Unable to parse HGVS notation '12:g.58142319A>C': Reference allele extracted from 12:58142319-58142319 (T) does not match reference allele given by HGVS notation 12:g.58142319A>C (A)",
wrong coordinates, alleles
no matches in VEP
server issues
Proposal:
Add new parameter for instance -n--note.
If have -n, add a new column:GenomicLocation Explanation.
(if user defines -e) In error report, add Error Message column using the "errorMessage" value.
Background:
"genomicLocationExplanation":"End position changes from 123 to 122, because end position should be the position of last deleted nucleotide.errorMessage, e.g."errorMessage": "Unable to parse HGVS notation '12:g.58142319A>C': Reference allele extracted from 12:58142319-58142319 (T) does not match reference allele given by HGVS notation 12:g.58142319A>C (A)",Proposal:
-n--note.-n, add a new column:GenomicLocation Explanation.-e) In error report, addError Messagecolumn using the "errorMessage" value.