[Vcftools-help] vcf-query not working as expected

[Cecilia <cmc...@gm...>]

Hi,

I'm new to use the vcf tools (version 0.1.5). I tried to retrieve SNPs in
region scaffold_10:800-1500 and executed this command:

 vcf-query samples.filtered.vcf -r scaffold_10:800-1500 > scaffold_10.vcf

The output file actually contains ALL SNPs in the input VCF file rather than
those in the specified region. Does anybody know why and how to fix it?

Thanks.

Here is a part of my input vcf file:

##fileformat=VCFv4.0
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Read depth for 1) forward
reference bases; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for 1) strand bias
(exact test); 2) baseQ bias (t-test); 3) mapQ bias (t); 4) tail distance
bias (t)">
##INFO=<ID=AF1,Number=1,Type=Float,Description="EM estimate of site allele
frequency without prior">
##INFO=<ID=AFE,Number=1,Type=Float,Description="Posterior expectation of
site allele frequency (with prior)">
##INFO=<ID=HWE,Number=1,Type=Float,Description="P-value for Hardy-Weinberg
equillibrium (chi-square test)">
##INFO=<ID=MQ,Number=1,Type=Integer,Descriptin="RMS mapping quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA
genotypes (R=ref,A=alt)">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
FORMAT  Sample1      Sample2
scaffold_10     41      .       A       G       59.3    .
DP=26;AF1=0.6664;CI95=0.5,0.75;DP4=8,8,2,7;MQ=37;PV4=0.23,6.3e-08,0.0017,1
GT:GL:DP:SP:GQ  0/1:-6.50,0.00,-25.50:24:7:
71      1/1:-2.90,-0.30,0.00:1:0:5
scaffold_10     55      .       A       G       3.36    .
DP=33;AF1=0.2929;CI95=0.25,0.5;DP4=14,10,1,7;MQ=38;PV4=0.041,1.9e-13,0.0019,1
GT:GL:DP:SP:GQ  0/1:-3.30,0.00,-25.50:30:10
:32     0/0:0.00,-0.60,-5.30:2:0:8
scaffold_10     57      .       T       C       16.3    .
DP=34;AF1=0.39;CI95=0.25,0.5;DP4=14,16,2,0;MQ=38;PV4=0.48,1,0.13,0.27
GT:GL:DP:SP:GQ  0/0:0.00,-9.00,-25.50:30:0:89   1/1
:-5.30,-0.60,0.00:2:0:4
scaffold_10     58      .       A       G       16.3    .
DP=34;AF1=0.39;CI95=0.25,0.5;DP4=14,17,2,0;MQ=38;PV4=0.23,1,0.13,0.27
GT:GL:DP:SP:GQ  0/0:0.00,-9.30,-25.50:31:0:92   1/1
:-5.30,-0.60,0.00:2:0:4
scaffold_10     83      .       C       T       16.3    .
DP=46;AF1=0.39;CI95=0.25,0.5;DP4=17,17,2,0;MQ=41;PV4=0.49,1,0.025,0.5
GT:GL:DP:SP:GQ  0/0:0.00,-10.20,-25.50:34:0:99  1/1
:-5.30,-0.60,0.00:2:0:4
scaffold_10     84      .       G       A       16.3    .
DP=46;AF1=0.39;CI95=0.25,0.5;DP4=17,17,2,0;MQ=41;PV4=0.49,1,0.025,0.45
GT:GL:DP:SP:GQ  0/0:0.00,-10.20,-25.50:34:0:99  1/1
:-5.30,-0.60,0.00:2:0:4

Regards,
Cecilia D