Vcftools gives error when extracting snps

Question

[BAGeno]

Hi,

I want to extract SNPs from vcf based on list of rsids. From this I used command vcftools --vcf <vcf_file> --snps <rsID_filename> --recode --recode-INFO-all

But it is giving me error.

stat error: No such file or directory
Error: Can't determine file type of --recode-INFO-all

Please tell me how to correct it.

[Pierre Lindenbaum]

this cannot be the command you used. This is just the synopsis. What is the command you typed in the terminal.

[BAGeno]

vcftools --vcf <Simon.dbsnp.annotated.vcf> --snps <RSIDs.txt> --recode --recode-INFO-all

This is the command I typed on terminal.

[Pierre Lindenbaum]

I would say you have no idea of what you're doing :-) Please read h.mon's answer and read about linux I/O redirection : https://www.digitalocean.com/community/tutorials/an-introduction-to-linux-i-o-redirection

[BAGeno]

I took command from here. Retrieve Single Vcf From List Of Snp Rs#

Answer 1

[h.mon]

You know < and > redirect input and output? Why don't you try the same command without them?

vcftools --vcf Simon.dbsnp.annotated.vcf --snps RSIDs.txt --recode --recode-INFO-all

[BAGeno]

I tried it and it worked. Thanks