Proportions covered is empty

[JoannaTan]

Hi,

I am using covviz to visualize the coverage across multiple samples.

However, the html file that I obtained does not have anything for the Proportions Covered tab.

This is the command that I used to run covviz

covviz indexcov.bed --ped samplechr.ped --sample-col sample_id --sex-col sex --output 100samples.html

I am running covviz using singularity.

Am I supposed to pass in the .roc file?

Thank you very much.

Hope to hear from you soon.

Best regards,
Joanna

[brwnj]

The latest version (1.1.1) no longer requires the .roc file. Can you verify this is a problem with the latest version?

[JoannaTan]

Hi @brwnj,

I have checked the version of covviz that I am using and it is version 1.1.1

covviz                    1.1.1                    pypi_0    pypi

[brwnj]

I added some indexcov output (2c7e4fd) that I have been using in testing the CLI. Can you verify the format of your indexcov.bed output against what's in covviz/data?

[JoannaTan]

Hi @brwnj,

Thank you for your help.

I realized that my indexcov.bed has the chr appended to the chromosome.

chr1    0       16384

I removed the chr and now it works.

Thank you very much.

[brwnj]

Thanks for reporting this because it's definitely a bug. I'll take a look at it tomorrow.

…

On Wed, Aug 28, 2019 at 8:21 PM JoannaTan ***@***.***> wrote: Hi @brwnj <https://github.com/brwnj>, Thank you for your help. I realized that my indexcov.bed has the chr appended to the chromosome. chr1 0 16384 I removed the chr and now it works. Thank you very much. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6?email_source=notifications&email_token=AAF77PWTZFXGV75HYCKCMWTQG4XCFA5CNFSM4IP3252KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5NANNI#issuecomment-525993653>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF77PUOZSIYZMILEUN5NB3QG4XCFANCNFSM4IP3252A> .

[brwnj]

fixed in 6cee85d.