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3 hours ago by

Hi,

I'm annotating my variants with VEP.
To test, I picked a random rsID and created a test input with all possible options with strand and without strand information.

But I get both 1 and -1 strands in my output and exactly the same amount of rows. Since I don't have transcript information, I also tried --pick_allele and --pick options but I still mostly get -1 strand results.

How does providing strand information play a role then?

Input with strand

1   45795027    45795027    C/G +
1   45795027    45795027    C/T +
1   45795027    45795027    G/G +
1   45795027    45795027    T/T +

Input without strand

1   45795027    45795027    C/G
1   45795027    45795027    C/T
1   45795027    45795027    G/G
1   45795027    45795027    T/T



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