filtered mutations

[mkinnaman]

Hi Christof!

Is there a way to see why a certain mutation might have been filtered out. Comparing your pipeline to an alternative one and trying to reconcile why some mutations were called in the alternative pipeline but filtered out by superfreq.

Thanks! Michael

[ChristofferFlensburg]

Hi, sorry I dropped the ball on this one. Is this issue still relevant? Essentially you load the allVariants.Rdata into R, located in the R directory of the individual, and there you have data frames of all variants (as supplied by the input VCF) in all samples pre filters. Anything where flag column is not an empty string is filtered.