Question: VCFtools command vcf-sort errors: main::error('Unknown parameter and main::parse_param
gravatar for wellingtonamaral
2.2 years ago by
wellingtonamaral0 wrote:

Hi, I'm new at preparing SNP data for analyses. I'm running vcf-sort and getting an error. Any ideas?

I have a new installation of everything .
Previously, I exported humanomniexpress-24v1 data from GenomeStudio, then ran: in Windows (PLINK v1.90b5): plink --ped CHR1.ped --map --recode vcf --out FILEchr1 in Ubuntu for Windows (VCFtools v0.1.15): vcftools --vcf FILE.vcf --chr 1 --out FILEchr1.vcf (I have not modified the data fie otherwise.)

I'm trying to run:

vcf-sort FILEchr1.vcf > FILEchr1s.vcf


vcf-sort FILEchr1.vcf | bgzip -c > FILEchr1.vcf.gz

and I'm getting the error:

Unknown parameter "FILEchr1.vcf". Run -h for help.
 at /usr/local/bin/vcf-sort line 20.
        main::error('Unknown parameter "FILEchr1.vcf". Run -h for help.\x{a}') called at /usr/local/bin/vcf-sort line 46
        main::parse_params() called at /usr/local/bin/vcf-sort line 10
snp vcftools vcf-sort • 1.2k views
ADD COMMENTlink modified 2.2 years ago by Pierre Lindenbaum126k • written 2.2 years ago by wellingtonamaral0

try vcf-sort < FILEchr1.vcf > FILEchr1s.vcf ?

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum126k
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