Re: [Vcftools-help] Clarification on --remove-indels option

[Warren W. K. <wkr...@gm...>]

Thanks.


On Wed, May 7, 2014 at 2:06 PM, Anthony Marcketta <
ant...@ei...> wrote:

> Winni,
>
> Yes these sentences mean the same thing, just with different wording. The
> sentence is just trying to clarify that these options only use the lengths
> of the reference and alternate alleles to determine if a site is an indel.
> The function does not inspect the bases within the sequence.
>
> --
> Anthony Marcketta
> Bioinformatics Analyst
> Department of Genetics
> Albert Einstein College of Medicine
> Van Etten B01
> Bronx, New York 10461
> ________________________________________
> From: Warren W. Kretzschmar [wkr...@gm...]
> Sent: Wednesday, May 07, 2014 6:29 AM
> To: vcftools-help
> Subject: [Vcftools-help] Clarification on --remove-indels option
>
> Hi,
> The vcftools manual page at <
> http://vcftools.sourceforge.net/man_latest.html>
> states the following about the --remove-indels option:
>
> > VARIANT TYPE FILTERING
> >
> > --keep-only-indels
> > --remove-indels
> >
> > Include or exclude sites that contain an indel. For these options
> "indel" means any variant that alters the length of the REF allele.
>
> I am confused about the wording. Does the last sentence mean exactly the
> same as the following sentence?
>
> 'For these options "indel" means any variant where the REF and any ALT
> allele have differing lengths.'
>
> Cheers,
> Winni
>
>