Arguments for data-profile

[24natasya]

I just want to ask, what arguments to i specify for --data-profile . Does is requires a vcf files or a truth file?

[dancooke]

The argument is a (CSV) file path where Octopus will write the data profile to, e.g.:

$ octopus -R ref.fa -I reads.bam -o calls.vcf --data-profile reads.profile.csv

You then use one or more profiles to generate new error models:

$ profiler.py -P reads.profile.csv -O reads.model

Then you can use this error model for variant calling:

$ octopus -R ref.fa -I reads.bam -o calls.vcf --sequence-error-model reads.model

There is no truth set needs to fit the error model.

[24natasya]

Thanks for your prompt reply. I really appreciate!

On Wed, Oct 9, 2019 at 4:53 PM Daniel Cooke notifications@github.com wrote:

The argument is a (CSV) file path where Octopus will write the data profile to, e.g.:

$ octopus -R ref.fa -I reads.bam -o calls.vcf --data-profile reads.profile.csv

You then use one or more profiles to generate new error models https://github.com/luntergroup/octopus/wiki/How-to:-Use-error-models:

$ profiler.py -P reads.profile.csv -O reads.model

Then you can use this error model for variant calling:

$ octopus -R ref.fa -I reads.bam -o calls.vcf --sequence-error-model reads.model

There is no truth set needs to fit the error model.

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[brentp]

@dancooke , one clarification on this, do the other arguments to octopus matter? E.g. if the data is from haploid clones, would the -C polyclone and other appropriate arguments matter?