Closed bozbezbozzel closed 1 year ago
Hi- --min-read-counts 0,0
doesn't discard any position based on depth in either normal or tumour. Instead, filtering for minimum (and maximum) depth in the normal sample is delegated to the --depth parameter (NB --depth
applies to the normal sample only - there is no filtering for tumour). This threshold is applied to the table of counts produced by snp-pileup via function filter_rcmat. Since the default is --depth 25 4000
the suggestion from FACETS vignettes is effectively maintained.
If I remember correctly, I set snp-pileup to 0,0 so that you compute the table of counts only once and later use the same pileup to play with various --depth
settings.
TL:DR: Because there is the --depth
parameter to do the same.
Hope this helps- I'm closing the issue but feel free to reopen.
Thanks for your explanation, that makes a lot of sense.
Basically the title, is there a reason this can't be adjusted via command line?
FACETS manual: https://raw.githubusercontent.com/mskcc/facets/master/vignettes/FACETS.pdf, see page 2 for recommended snp-pileup settings.