Extract each annotation in 'info' column in snpEff output
0
1
Entering edit mode
6.7 years ago
jan ▴ 170

Hi,

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 .

snpEff sequencing output • 3.5k views
1
Entering edit mode

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.

2
Entering edit mode

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

1
Entering edit mode

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