Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: VariantsToTable? Extract AF from INFO column of VCF
0
gravatar for rich_jp
2.6 years ago by
rich_jp • 0
United Kingdom
rich_jp • 0 wrote:

Hi all, I would like to extract the AF from the INFO column of GATK Unified Genotyper VCF files (e.g. in tabular format) for downstream analysis. This can be done with GATK VariantsToTable for example but how can this be done inside Galaxy (not finding a good tool wrapper for this)?

Cheers, Richard
vcf • 1.2k views
ADD COMMENT • link •
modified 2.6 years ago • written 2.6 years ago by rich_jp • 0

Both work great - thanks Björn :)

Richard

ADD REPLY • link written 2.6 years ago by rich_jp • 0

You can accept the answer as correct. This will enable other to find it easier. Thanks!

ADD REPLY • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k
2
gravatar for Bjoern Gruening
2.6 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Richard,

you could use use the cut tools to extract the INFO column. And than use the tool "Convert delimiters to TAB" to get your key - values.

Alternatively you can try this tool:

https://toolshed.g2.bx.psu.edu/repository?repository_id=c312e18db2cc2487

Hope this helps, Bjoern
ADD COMMENT • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour