Opened 10 months ago

Closed 8 months ago

#1215 closed enhancement (fixed)

Include mutation signature analysis in the variant calling pipeline

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.25
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

A mutation signature can be calculated from the filtered variants VCF. See https://cancer.sanger.ac.uk/cosmic/signatures_v2

The calculations are done with an R script and generate PDF plot and a text file with a score for each of 30 signature patterns.

The R script should be included in the variant call script and the pdf and text file should be stored and attached to the rawbioassay item together with the existing VCF files. The scores should be imported to annotations: MutationSignature1, ... MutationSignature30.

Change History (9)

comment:1 Changed 9 months ago by Nicklas Nordborg

Status: newaccepted

comment:2 Changed 9 months ago by Nicklas Nordborg

In 5792:

References #1215: Include mutation signature analysis in the variant calling pipeline

Adding annotation types MutationSignature1, ..., MutationSignature30 to the installation wizard.

comment:3 Changed 9 months ago by Nicklas Nordborg

In 5793:

References #1215: Include mutation signature analysis in the variant calling pipeline

0-pad names so that we get MutationSignature01 instead. It is nicer to have the annotations sorted in the expected order.

comment:4 Changed 9 months ago by Nicklas Nordborg

In 5794:

References #1215: Include mutation signature analysis in the variant calling pipeline

Implemented support for parsing the output file with scores for the mutation signatures.

comment:5 Changed 9 months ago by Nicklas Nordborg

In 5795:

References #1215: Include mutation signature analysis in the variant calling pipeline

Implemented a step in the variant calling pipeline for calling the mutation_signature.R script.

comment:6 Changed 9 months ago by Nicklas Nordborg

In 5796:

References #1215: Include mutation signature analysis in the variant calling pipeline

Adding pipeline script for analyzing COSMIC mutation signature.

comment:7 Changed 9 months ago by Nicklas Nordborg

In 5807:

References #1215: Include mutation signature analysis in the variant calling pipeline

Added a wrapper shell script for starting R scripts with R 3.6.2. We need to set PATH and LD_LIBRARY_PATH so that R can find the correct versions.

comment:8 Changed 8 months ago by Nicklas Nordborg

In 5809:

References #1215: Include mutation signature analysis in the variant calling pipeline

Use the wrapper script to start the mutation signature R script.

comment:9 Changed 8 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed
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