[Biopython] Parsing SnpEff's VCF file
Mic
mictadlo at gmail.com
Tue Apr 29 10:28:39 UTC 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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