Trouble with DeepVariant after running Minimap2

[moyarod]

Hello,

I am trying to run Deepvariant in Galaxy with a bam file from Minimap2 but it sais there is a problem with the vcf format. Quite new using these tools and I am lost! please anyone could help me?

[kishwarshafin]

Hello, as you can see the error message is "samtools: command not found". Can you please see if there's a way you can install samtools for your environment?

[moyarod]

Thanks for answering. I forgot to say that the samtools are already installed.

[kishwarshafin]

@moyarod ,

In that case, it would be ideal if you seek help from the galaxy community: https://help.galaxyproject.org/ as this is a platform-specific error and we can't reproduce this on our end.