|
From: Anthony M. <ant...@ei...> - 2014-05-07 13:07:16
|
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 |