PASS Variants Can Have Allele Frequency Exactly Zero

Illumina / strelka

Strelka2 germline and somatic small variant caller

GNU General Public License v3.0

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PASS Variants Can Have Allele Frequency Exactly Zero #154

Open DarioS opened 4 years ago

DarioS commented 4 years ago

Some variants only have Tier 2 reads supporting them but PASS. This results in the strange situation of having a passing somatic variant with a high EVS score in the filtered VCF file, but an allele frequency of 0.00.

likelet commented 4 years ago

I openned a similar issue but have not been resolved yet https://github.com/Illumina/strelka/issues/12