[Biopython] Parsing SnpEff's VCF file

Mic mictadlo at gmail.com
Tue Apr 29 06:28:39 EDT 2014


Hello,
SnpEff created a new VCF file which looks like this line

DA_v3.0    1252    DA0000001    G    T    3.0    .
DP=12;EFF=DOWNSTREAM(MODIFIER|||||Q3TPR7|||Transcript_DA_0011r.4||1),DOWNSTREAM(MODIFIER|||||Q8GYX9|||Transcript_DA_0011r.2||1),INTERGENIC(MODIFIER||||||||||1)
GT:DP    0/0:3    ./.:0    ./.:0    1/1:3    0/0:3    0/0:1    0/0:2
./.:0

I found Gemini project which contains a SnpEff class (
https://github.com/arq5x/gemini/blob/master/gemini/snpEff.py ).

However, I am not quite sure how to use snpEff.py outside Gemini project in
order to parse the whole SnpEff's VCF file. Or does BioPython provide a
parser?

Thank you in advance,


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