Question: Vcftools gives error when extracting snps
0
gravatar for BAGeno
19 months ago by
BAGeno110
BAGeno110 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 • 880 views
ADD COMMENTlink written 19 months ago by BAGeno110
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 19 months ago by Pierre Lindenbaum116k
vcftools --vcf <Simon.dbsnp.annotated.vcf> --snps <RSIDs.txt> --recode --recode-INFO-all

This is the command I typed on terminal.

ADD REPLYlink written 19 months ago by BAGeno110
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 19 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink modified 19 months ago • written 19 months ago by BAGeno110
3
gravatar for h.mon
19 months ago by
h.mon23k
Brazil
h.mon23k 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 19 months ago by h.mon23k

I tried it and it worked. Thanks

ADD REPLYlink written 19 months ago by BAGeno110
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