Entering edit mode
6.4 years ago
wellingtonamaral
•
0
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 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
try
vcf-sort < FILEchr1.vcf > FILEchr1s.vcf
?