problem with var and var.ex

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Lili

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May 22, 2013, 5:17:47 PM5/22/13
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Hi,
I have a pseq project by reading in several single VCF files. I want to include/exclude some regions for analysis and I uploaded a var file looks like this:
REG    test    chr22:16220000..16242500
REG    test    chr22:17150000..17394100
...

When I run command below I can get SNPs in target region for sample1, but not the rest of samples.
pseq proj1 write-vcf --mask var=test

#CHROM

POS

FORMAT

sample1

sample2

sample3

sample4

chr22

16222618

GT:GQ

1/0:90

.:.

.:.

.:.

chr22

16224667

GT:GQ

0/1:83

.:.

.:.

.:.

chr22

16224740

GT:GQ

0/1:95

.:.

.:.

.:.

 

When I run command below, I can exclude SNPs in target region in sample1, not the rest of them.
pseq proj1 v-view --mask var.ex=test

#CHROM

POS

FORMAT

sample1

sample2

sample3

sample4

chr22

16222618

GT:GQ

.:.

1/0:90

1/0:90

1/0:90

chr22

16224667

GT:GQ

.:.

0/1:83

0/1:83

0/1:83

chr22

16224740

GT:GQ

.:.

0/1:95

0/1:95

0/1:95


It looks like the var and var.ex only works on the first sample. Is there anything wrong with my code?
Please advice. Thanks.

Lili

 

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