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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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--min-read-counts hardcoded to 0,0 instead of 25,0 as recommended by FACETS manual #50

Closed bozbezbozzel closed 1 year ago

bozbezbozzel commented 1 year ago

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.

dariober commented 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.

bozbezbozzel commented 1 year ago

Thanks for your explanation, that makes a lot of sense.