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

[Anthony M. <ant...@ei...>]

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