Question: VariantsToTable? Extract AF from INFO column of VCF
0
gravatar for rich_jp
2.6 years ago by
rich_jp0
United Kingdom
rich_jp0 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 COMMENTlink modified 2.6 years ago • written 2.6 years ago by rich_jp0

Both work great - thanks Björn :)

Richard

ADD REPLYlink written 2.6 years ago by rich_jp0

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

ADD REPLYlink written 2.6 years ago by Bjoern Gruening5.1k
2
gravatar for Bjoern Gruening
2.6 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 COMMENTlink written 2.6 years ago by Bjoern Gruening5.1k
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