[Vcftools-help] (no subject)

[Younes M. <mi...@ua...>]

Hello everyone,

I am using this command to extract SNPs in chromosome 1 only

vcftools --vcf geno_final2.vcf --chr 1 --out subset

Here is the log file:

VCFtools - v0.1.12b
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
        --vcf geno_final2.vcf
        --chr 1
        --out subset

Second Header entry should be POS:
Third Header entry should be ID: POS
Fourth Header entry should be REF: ID
Fifth Header entry should be ALT: REF
Sixth Header entry should be QUAL: ALT
Seventh Header entry should be FILTER: QUAL
Eighth Header entry should be INFO: FILTER
Ninth Header entry should be FORMAT: INFO
After filtering, kept 9689 out of 9689 Individuals
After filtering, kept 0 out of a possible 19 Sites
No data left for analysis!
Run Time = 0.00 seconds


The geno_final file is like this:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HO840M3001697380
HO840M300169749
chr1 100021883 BTA-45212-no-rs C T 999 . . GT 1/1 1/0

I have 6 SNPs in CHR 1, however VCFTOOLS gives me no sites.

I would be highly appreciated if you could help me on this please?

Best Regards,
Younes