Question: Vcftools gives error when extracting snps
0
gravatar for BAGeno
2.1 years ago by
BAGeno140
BAGeno140 wrote:

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.

snp vcftools • 1.1k views
ADD COMMENTlink written 2.1 years ago by BAGeno140
1

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

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k
vcftools --vcf <Simon.dbsnp.annotated.vcf> --snps <RSIDs.txt> --recode --recode-INFO-all

This is the command I typed on terminal.

ADD REPLYlink written 2.1 years ago by BAGeno140
1

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

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum122k

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

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by BAGeno140
3
gravatar for h.mon
2.1 years ago by
h.mon27k
Brazil
h.mon27k wrote:

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
ADD COMMENTlink written 2.1 years ago by h.mon27k

I tried it and it worked. Thanks

ADD REPLYlink written 2.1 years ago by BAGeno140
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