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the Filter field in gvcf file created by HaplotypeCaller


I ran HaplotypeCaller on few projects.
In the output gvcf file, the "Filter" field is always "."
From the gvcf header, I understand that Filter can also be "LowQual". from the documentation, I understand that it depends on the stand_emit_conf and stand_call_conf parameters. I used stand_emit_conf 10 and stand_call_conf 30.
Do I understand this field correct? When this filter is active?

Thank you,

Best Answer


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