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mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Output VNTR that raised errors during genotyping in VCF and BED format #59

Closed Jong-hun-Park closed 2 years ago

Jong-hun-Park commented 2 years ago

Description

adVNTR adds logs for VNTR that raised errors during genotyping but skips outputting results. This behavior makes it challenging to debug which VNTR has issues.

Solution

Output the results even for VNTR that raised errors during genotyping. The output is "Error" for BED or plain text format. For VCF, we use the "Filter" column to indicate that this VNTR had an error during the genotyping step.

Jong-hun-Park commented 2 years ago

The frameshift option has a specific format, and adVNTR doesn't support VCF or BED output format for the option. That's a good point, and we should update them later in a different branch.