genome/genome — pull request #118 by gatoravi (2014-10-20 01:12:39+00:00)
Title: Clinseq updates - bamreadcount parameters in clinseq,  snvindel report updates, sciclone_plots, mutation_spectrum, manual cnview results.

This PR adds some important updates to ClinSeq. These should ideally be separate pull-requests for each feature but these issues are interlinked and I started working on these before we moved to PR's. The 'Files -Changed' tab of the PR would probably be the easiest way to look at these changes.

The updates that this PR adds to ClinSeq are,
1. Versioning of bam-readcount parameters in ClinSeq.
The minimum mapping quality and base quality used for read-counting are now set in the ClinSeq processing-profiles. The parameter is "sireport_min_mq_bq" which a list of comma separated mq,bq pairs delimited by semicolons, so like 1,1:10,20:20,30 etc

2. SnvIndel Report
SNVIndel report filtering parameters are also tracked in the processing-profile. The parameters are sireport_min_tumor_vaf, sireport_max_normal_vaf and sireport_min_coverage. These are all +ve integers indicating the cutoffs for producing the final filtered snv_indel_report. SnvIndel report also now has a column indicating the datatype where the variant was called(wgs, exome, rnaseq etc) and tracks why a variant was filtered out. A tool summarizing the number of variants in the snv_indel_report was also added. ('Converge/SummarizeSnvIndelReport.pm').

3. SciClone Plots
Add a tool which uses the snv_indel_report output to produce 1d sci-clone plots in ClinSeq. Separate sci-clone plots are produced for different read-counting parameters set in the processing-profile. In the ClinSeq build these are under the clonality/sciclone folder under different bq, mq cutoffs like "b20_q1/"

4. Mutation Spectrum results
Mutation spectrum now uses the snv_indel_report results as well instead of using the results from somatic-variation. This allows mutation spectrum results to be generated from the set of filtered variants which we are more confident about. Separate directories using the results from the various cutoffs are generated just like the sciclone results.

6. Minor updates
The runCnView step run on results from somatic variation builds using CopyCat which are stored in different files compared to cnvhmm.
Shared ClinSeq subroutines were added/moved to ClinSeq/Util.pm.
FileAccessors to obtain certain files from ClinSeq were also added.

We totally understand that reviewing all these changes would be an immense time-suck especially if you haven't worked with ClinSeq before but we would appreciate all feedback we can get on these since these changes could definitely be improved and this is a first-pass.