User: aurora

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aurora0
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Posts by aurora

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Comment: C: VCF file help
... After I add that line the result is just one line: 1 10048 . C CCT . CA VT=INS;VLS=5;ANNOVAR_DATE=2016-02-01;Func.refGene=intergenic;Gene.refGene=NONE,DDX11L1;GeneDetail.refGene=dist\x3dNONE\x3bdist\x3d1826;ExonicFunc.refGene=.;AAChange.refGene=.;ALLELE_END GT:DP:AD:BQ:SS:SSC:MQ60 0/0:66:.,0:.:0:.: ...
written 9 months ago by aurora0
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Comment: C: VCF file help
... Sorry I thought that I need to combine them because it is showing me error info_field_line = line.split("\t")[7] IndexError: list index out of range and I tried with other indexes, still the same ...
written 9 months ago by aurora0
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Comment: C: VCF file help
... Oh I did't see this related post.. thank you, for helping :) So if I combine these two scripts I should obtain something like: import sys import re def parse_vcf(vcf_file): with open(vcf_file, 'r+') as vcf_f: for line in vcf_f: if line[0] != '#': ...
written 9 months ago by aurora0
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VCF file help
... Hello Biostars, I am doing project with vcf files and I need your help. After annotation in Annovar I used python to extract gene names, exonic function and aa change. I want to remove from output genes that do not have exonic function and aa change (ExonicFunc.refGene = . ; AAChange.refGene = . ) ...
vcf python script written 9 months ago by aurora0 • updated 9 months ago by Bastien Hervé2.7k

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