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