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

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

I have to backtrack a bit.  It seems like the previous command never created the needed file upon common to filter by chromosome.  Hence my input file FILEchr1.vcf was never created.  Though, looking at the log file, it looks like it should have creamer the file.    The file is not in the directory.  This is the log from running —
vcftools —vcf File.vcf —chr 1 —out FILEchr1.vcf :

VCFtools - 0.1.15
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
	--vcf MIDUS.vcf
	--chr 1
	--out MIDUSchr1.vcf

After filtering, kept 2129 out of 2129 Individuals
After filtering, kept 58404 out of a possible 716503 Sites
Run Time = 27.00 seconds

Any ideas why it didn’t create the file?
Thanks again!!

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/>

> On Dec 2, 2017, at 8:40 AM, Wellington Z. Amaral <wa...@wi...> wrote:
> 
> 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/>
>