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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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Variant quality filter empties the VCF when users don't provide "PASS" designations #4

Closed coledeisseroth closed 5 months ago

coledeisseroth commented 7 months ago

Describe the bug The variant quality filtering step requires the FILTER column in the VCF to be labeled as "PASS". If this designation is not provided in a VCF (which sometimes, it is not), AIM will throw away all of the variants.

Expected behavior Filtering out the low-quality variants

Input data A VCF file. In my case, the "FILTER" column of the VCF was always labeled as "."

Genome build hg38--but this doesn't matter

Screenshots or pipeline output I cannot give a screenshot.

Additional context That is all.

sasidharPasupuleti commented 5 months ago

The bug has been resolved.

Solution : if "PASS" filtering step results in zero variants ( which also means there were no variants marked "PASS" or had "." ) all variants that were input are considered for the remaining steps by AIM.