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nif:beginIndex
  • 0 (xsd:integer)
nif:broaderContext
nif:endIndex
  • 574 (xsd:integer)
nif:isString
  • QC over all samples (INFO column) was done as follows: a) for SNVs, variants were filtered for QD < 2.0, FS > 60.0, MQ< 40.0, MQRankSum < –12.5, ReadPosRankSum < –8.0, DP <10.0, GQ_MEAN < 20.0, VQSLOD < 0, more than 5% missingness, ABHet > 0.75 or < 0.25 and deviation from Hardy-Weinberg equilibrium (Phred scale p-value of > 20); b) for INDELs, the same was done as for SNVs except for the following parameters for variant filtration: QD <2.0, FS >200.0, ReadPosRankSum < –20.0, DP <10.0, GQ_MEAN <20.0, missingness <5%, Hardy-Weinberg Phred scale value of >20, VQSLOD >0.
rdf:type