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Filtering Not Generating Expected Result
As many members have suggested I am using a standard method of running through VariantFiltration to change samples with low depth to missing genotype using -G_filter "DP<4" -G_filterName "SampleDepthFilter4" --setFilteredGtToNocall.
Then using SelectVariants to filter by MAF and Missing%s using allele numbers with the resulting file using --selectexpressions "AF>0.1" --selectexpressions "AF<0.9" --selectexpressions "AN>140" --restrictAllelesTo BIALLELIC --selectTypeToExclude INDEL.
However when I'm not going through and looking at the results, I see that in almost all cases the missing percentages are much higher than what I was theoretically filtering for with Allele Number greater than 140, ie 70 individuals. It seems that it is not taking into account the genotypes that have been changed over to missing based on the sample depth filter, even though it is using the resulting file from the VariantFiltration step. Why is filtering not performing as anticipated?