Question: Extract each annotation in 'info' column in snpEff output
gravatar for jan
4.6 years ago by
Sydney, Australia
jan130 wrote:


I have used snpEff to annotate my vcf file. I previously use Annovar to annotate my vcf file and the  fields are nicely separated in tabular forms, hence making it easy to extract information for further analysis.

snpEff annotation is written in 'info' column in one line separated by a pipe ' | '  , making it difficult to extract certain information . Is there a tool to separate each annotation into separate tab ? I tried to write a python script (with a very limited knowledge about programming ) but it gets messy .

sequencing output snpeff • 2.3k views
ADD COMMENTlink written 4.6 years ago by jan130

awk would probably be able to do it efficiently. Exactly which information do you want? Do you need the tab-delimited stuff at the beginning, or the semi-colon-delimited values, etc?

A simple way would be to just to specify your field separators at the start of an awk command, and split everything into tab-delimited columns.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Joseph Pearson450

I just found out about snpSift and the tool suits my work

ADD REPLYlink written 4.6 years ago by jan130

That looks like a useful tool, thank you for making me aware of snpSift!

ADD REPLYlink written 4.6 years ago by Joseph Pearson450
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