On 4 Mar 2016, at 12:11, Ryan Kevin <[email protected]> wrote:
> In version 0.1.19 of bcftools view there is the setting:
>
> -N which is defined as Skip sites where the REF field is not A/C/G/T
>
> I am currently running version 1.2 of bcftools and I realised that I still
> have -N set when calling bcftools call. However -N is not in the
> documentation any more suggesting it has been deprecated. However there is no
> error message associated with leaving the setting in so I am not sure is
> there any difference between leaving -N set or not
(The current release of bcftools is 1.3 BTW.)
> Can anyone shed some light on whether setting -N is likely to make any
> difference to the calling and if so what will that be or does -N have no
> effect and in 1.2 the function of -N occurs by default any way?
Examining the current bcftools code shows that -M/--keep-masked-refs and
-N/--skip-Ns are opposites and the default is now -N. So it's the latter: -N
means the same thing as it used to, and using it mostly has no effect as it
occurs by default.
It would be good to add -N/--skip-Ns to the documentation.
John
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