Question: Does The Vcffilter Tool Work On String Type Info Tags?
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gravatar for dwaggott
7.4 years ago by
dwaggott290
United States
dwaggott290 wrote:

Hey,

vcflib looks great! To get started I need a bit of direction on filtering using vcffilter. Specifically, does it work on string type info tags? Also, can one group expressions similar to test5 below? I tried it on dbSNP138 clinical and ran into some problems.

Best, Daryl

### dbSNP138
#ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/

wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/clinvar_20130808.vcf.gz 
wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/clinvar_20130808.vcf.gz.tbi

### test1 and test2 work but not test3-5
vcffilter -f "PM" clinvar_20130808.vcf.gz > test1.vcf  # PM is a flag
vcffilter -f "COMMON = 1" clinvar_20130808.vcf.gz > test2.vcf  # COMMON is a integer
vcffilter -f "CLNSIG = 4" clinvar_20130808.vcf.gz > test3.vcf #  CLINSIG and CLNORIGIN are strings
vcffilter -f "CLNORIGIN = 4" clinvar_20130808.vcf.gz > test4.vcf 
vcffilter -f "(COMMON = 0) & (MUT | PM | CLNSIG = 3 | CLNSIG = 4 | CLNORGIN = 4 | CLNORGIN = 32)"   00-All.vcf.gz > test5.vcf
vcf • 1.7k views
ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by dwaggott290

So the problem is that you have an integer in your filter, but it's a String type in the file...

ADD REPLYlink written 6.4 years ago by Erik Garrison2.3k
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