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!
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pifferdavide
I believe you can simply use --snp multiple times, one for each snp. Alternatively, you can read from a file using --snps.
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Sean Davis
Thanks! It works now
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pifferdavide
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.
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Sean Davis
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