Add option to filter VCF output to PASS entries about exomiser

[buske]

We're switching over to using the variants.tsv output, and here too it would be useful to have it pre-filtered to PASS rows, since this leads to a reduction in file size of ~100x for an average exome.

[visze]

If we implement this cli option it should affect every output. Otherwise it will be confusing for the user.

But in piplines (or if you have a bash start script) it will be easy to implement a postprocessing step like:
cat variants.tsv | egrep "^#|PASS" > variants_filtered.tsv

(maybe Pass instead of PASS. Can't remeber it.)

[buske]

Agreed. Yep, that's exactly what we do. It is definitely not a critical issue at all, just a minor feature request. It was the ~200 mb of disk usage I was trying to avoid, since it slows things down when we're processing hundreds of VCF files, especially if we wanted to run them all in batch with --batch-settings (since you're going to have accumulated several hundred GB of data by the end, when all you care about is several hundred MB of it). :)

[julesjacobsen]

Made a snappy new command for the console:

output-pass-variants-only

This defaults to false when not mentioned. Can be called from a settings file like so:

output-pass-variants-only=true

or from the command line

--output-pass-variants-only

[julesjacobsen]

That was a lot of code for what could be done as a grep or awk command! Damn!

[visze]

:-)

2015-03-31 16:46 GMT+02:00 Jules Jacobsen [email protected]:

That was a lot of code for what could be done as a grep or awk command!
Damn!

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#35 (comment).

[buske]

:( Sorry!