[Vcftools-help] vcf-sort errors: main::error('Unknown parameter and main::parse_param

[Wellington Z. A. <wa...@wi...>]

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


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 CHR.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 or 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




Wellington Amaral, M.S.
Biopsychology Doctoral Candidate
University of Wisconsin - Madison

Coe Psychoneuroimmunology Lab
Harlow Center for Biological Psychology
22 N. Charter Street, Rm. 155
Madison, WI   53715

wa...@wi... <mailto:wa...@wi...>
Voicemail: 608-432-5764
Facsimile: 608-262-6020

To schedule a meeting:
wellington.appointlet.com <http://wellington.appointlet.com/>