Implement WGS structural variant calling pipeline

[Nicklas Nordborg]

This should be similar to the existing WGS variant calling, but check for structural variants instead. gridss (​https://github.com/PapenfussLab/gridss) is a possible candidate to use for the variant calling, but we probably need some post processing of the results as well.

[Nicklas Nordborg]

In 7924:

References #1623: Implement WGS structural variant calling pipeline

Added an item list, pipeline and annotation type category for structural variant calls. New wizards on the start page.

[Nicklas Nordborg]

In 7925:

References #1623: Implement WGS structural variant calling pipeline

Started to implement this wizard. Tumor-Normal pairs can be selected and submitted to the cluster but the script doesn't do anything.

[Nicklas Nordborg]

In 7926:

References #1623: Implement WGS structural variant calling pipeline

Added a container with gridss.

[Nicklas Nordborg]

In 7927:

References #1623: Implement WGS structural variant calling pipeline

Started to implement the variant calling script. First step is to copy the tumor and normal BAM files. In debug mode it is possible to work with a subset (chr1 default).

[Nicklas Nordborg]

In 7928:

References #1623: Implement WGS structural variant calling pipeline

Added the gridss pre-processing step.

[Nicklas Nordborg]

In 7929:

References #1623: Implement WGS structural variant calling pipeline

Implemented the "assemble" step.

[Nicklas Nordborg]

In 7930:

References #1623: Implement WGS structural variant calling pipeline

Implemented the variant calling step.

[Nicklas Nordborg]

In 7931:

References #1623: Implement WGS structural variant calling pipeline

Implemented the somatic filtering step.

[Nicklas Nordborg]

In 7932:

References #1623: Implement WGS structural variant calling pipeline

Organising result files and linking them in BASE to the variant call bioassay.

[Nicklas Nordborg]

In 7944:

References #1623: Implement WGS structural variant calling pipeline

Added a step that create bedpe and bed files from the VCF. The bedpe file is needed for the mutational signature step.

[Nicklas Nordborg]

In 7946:

References #1623: Implement WGS structural variant calling pipeline

Added annotations also for the number of single breakends.

[Nicklas Nordborg]

In 7960:

References #1623: Implement WGS structural variant calling pipeline

Added a manual confirmation wizard for structural variants. The VCF file is currently linked to the regular VCF viewer which doens't work so good for this kind of VCF so we need something different here.

[Nicklas Nordborg]

In 7961:

References #1623: Implement WGS structural variant calling pipeline

Fixes some issues with the "Start structural variant call" wizard.

[Nicklas Nordborg]

In 7962:

References #1623: Implement WGS structural variant calling pipeline

Added support for auto-confirmation after structural variant calling.

[Nicklas Nordborg]

In 7971:

References #1623: Implement WGS structural variant calling pipeline

Added a circos plot of the breakends to the output.

[Nicklas Nordborg]

In 7972:

References #1623: Implement WGS structural variant calling pipeline

Add a check for number of variants before trying to plot since it will crash if there is no remaining links.

[Nicklas Nordborg]

In 7973:

References #1623: Implement WGS structural variant calling pipeline

Plotting stopped working inside the if statement. Turned out that we need an explicit print() statement.

[Nicklas Nordborg]

In 7974:

References #1623: Implement WGS structural variant calling pipeline

Adding thumbnails of the circos plots to the list page and view page for structural variant calls.

[Nicklas Nordborg]

In 7975:

References #1623: Implement WGS structural variant calling pipeline

Add a link to the circos plot in the manual confirmation wizard.

[Nicklas Nordborg]

In 7979:

References #1623: Implement WGS structural variant calling pipeline

The assembly.sv.bam file is added as a link instead of a BAM file since it is not any real data in it.

[Nicklas Nordborg]

In 7980:

References #1623: Implement WGS structural variant calling pipeline

Structural variants should not be indexed by the variant search extension since they are not supported.