Allele 2 column all 0

[Amanda Owings]

This is probably a very basic problem, but we're new to lobSTR. We tried to get some STR data from the Simons data set for a few populations and the resulting file only had one column with an STR repeat value in it and the allele 2 column only had 0s. Did we do something wrong? What’s best way to transpose vcf from Simons data into calls with 2 alleles?

Thanks!

[Melissa Gymrek]

Hello,

I encourage you to use HipSTR instead, which has many new features and is more reliable: https://github.com/tfwillems/HipSTR

Best,

~M

On Wed, Jan 15, 2020 at 10:22 AM Amanda Owings <amanda...@gmail.com> wrote:

This is probably a very basic problem, but we're new to lobSTR. We tried to get some STR data from the Simons data set for a few populations and the resulting file only had one column with an STR repeat value in it and the allele 2 column only had 0s. Did we do something wrong? What’s best way to transpose vcf from Simons data into calls with 2 alleles?

Thanks!

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