Question: how do I write a string of SNPs on vcftools?
2
gravatar for pifferdavide
4.1 years ago by
pifferdavide90
Italy
pifferdavide90 wrote:

The "snp" command works with only 1 snp, but if I type 2 SNPs, it does not, as from output below. VCF tools manual says snp <string> but how do I write the string of several SNPs? rs236330rs236330 or rs236330-rs236330?

I tried the command "snps" to include a list of SNPs from a file but it doesn't recognize the command

--vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf
    --chr 1
    --freq
    --out chr1_analysis
    --snp rs236330-rs236322

After filtering, kept 2504 out of 2504 Individuals
Outputting Frequency Statistics...
After filtering, kept 0 out of a possible 6468094 Sites
No data left for analysis!
 

vcftools 1000 genomes vcf • 1.6k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by pifferdavide90
2
gravatar for Sean Davis
4.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

I believe you can simply use '--snp' multiple times, one for each snp.  Alternatively, you can read from a file using '--snps'.

ADD COMMENTlink written 4.1 years ago by Sean Davis25k
0
gravatar for pifferdavide
4.1 years ago by
pifferdavide90
Italy
pifferdavide90 wrote:

Thanks! It works now

ADD COMMENTlink written 4.1 years ago by pifferdavide90
1

Good to know.  As an aside, better than adding another answer, you can simply comment.  Also, if an answer "works" for you,  accept the answer so that other folks know that the question has been answered satisfactorily.

ADD REPLYlink written 4.1 years ago by Sean Davis25k
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