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dantaki / SV2

Support Vector Structural Variation Genotyper
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Test data run #3

Closed fritzsedlazeck closed 6 years ago

fritzsedlazeck commented 6 years ago

Hi, we tried to run the test data that you provide with hg19 using the commands that you suggest.

All of the variance in the resulting file show GENOTYPEFAIL. I have checked for differences in the chr names, but they appear to be the same.

Do you have any advice? Thanks Fritz

dantaki commented 6 years ago

The BAM file is severely downsampled. The tutorial is merely an example on how to run SV2, not an example of genotype scoring or filtering.

In the tutorial wiki page it states

Note: This tutorial is merely an example. The BAM file has been down-sampled to low depths (<1x) inadequate for genotyping.

I hope this answers your question.

fritzsedlazeck commented 6 years ago

thanks. Fritz