MAVIS (Full) Tutorial
The following tutorial is an introduction to running MAVIS. You will need to download the tutorial data. Additionally the instructions pertain to running MAVIS on a SLURM cluster. This tutorial will require more resources than the mini-tutorial above.
Getting the Tutorial Data
The tutorial data can be downloaded from the link below. Note that it may take a while as the download is \~29GB
wget http://www.bcgsc.ca/downloads/mavis/tutorial_data.tar.gz
tar -xvzf tutorial_data.tar.gz
The expected contents are
| Path | Description |
|---|---|
| README | Information regarding the other files in the directory |
| L1522785992_expected_events.tab | The events that we expect to find, either experimentally validated or 'spiked' in |
| L1522785992_normal.sorted.bam | Paired normal library BAM file |
| L1522785992_normal.sorted.bam.bai | BAM index |
| L1522785992_trans.sorted.bam | Tumour transcriptome BAM file |
| L1522785992_trans.sorted.bam.bai | BAM index file |
| L1522785992_tumour.sorted.bam | Tumour genome BAM file |
| L1522785992_tumour.sorted.bam.bai | BAM index file |
| breakdancer-1.4.5/ | Contains the BreakDancer output which was run on the tumour genome BAM file |
| breakseq-2.2/ | Contains the BreakSeq output which was run on the tumour genome BAM file |
| chimerascan-0.4.5/ | Contains the ChimeraScan output which was run on the tumour transcriptome BAM file |
| defuse-0.6.2/ | Contains the deFuse output which was run on the tumour transcriptome BAM file |
| manta-1.0.0/ | Contains the Manta output which was run on the tumour genome and paired normal genome BAM files |
Downloading the Reference Inputs
Run the following to download the hg19 reference files and set up the environment variables for configuring MAVIS
wget https://raw.githubusercontent.com/bcgsc/mavis/master/tools/get_hg19_reference_files.sh
bash get_hg19_reference_files.sh
source reference_inputs/hg19_env.sh
Generating the Config File
The config command does most of the work of creating the config for you but there are a few things you need to tell it
- Where your bams are and what library they belong to
--library L1522785992-normal genome normal False tutorial_data/L1522785992_normal.sorted.bam
--library L1522785992-tumour genome diseased False tutorial_data/L1522785992_tumour.sorted.bam
--library L1522785992-trans transcriptome diseased True tutorial_data/L1522785992_trans.sorted.bam
- Where your SV caller output files (events) are
If they are raw tool output as in the current example you will need to use the convert argument to tell MAVIS the file type
--convert breakdancer tutorial_data/breakdancer-1.4.5/*txt breakdancer
--convert breakseq tutorial_data/breakseq-2.2/breakseq.vcf.gz breakseq
--convert chimerascan tutorial_data/chimerascan-0.4.5/chimeras.bedpe chimerascan
--convert defuse tutorial_data/defuse-0.6.2/results.classify.tsv defuse
--convert manta tutorial_data/manta-1.0.0/diploidSV.vcf.gz tutorial_data/manta-1.0.0/somaticSV.vcf manta
Note
For older versions of MAVIS the convert command may require the path to the file(s) be quoted and the strandedness be specified (default is False)
- Which events you should validate in which libraries
For this example, because we want to determine which events are germline/somatic we are going to pass all genome calls to both genomes. We can use either full file paths (if the input is already in the standard format) or the alias from a conversion (the first argument given to the convert option)
--assign L1522785992-trans chimerascan defuse
--assign L1522785992-tumour breakdancer breakseq manta
--assign L1522785992-normal breakdancer breakseq manta
Putting this altogether with a name to call the config, we have the command to generate the pipeline config. You should expect this step with these inputs to take about \~5GB memory.
mavis config \
--library L1522785992-normal genome normal False tutorial_data/L1522785992_normal.sorted.bam \
--library L1522785992-tumour genome diseased False tutorial_data/L1522785992_tumour.sorted.bam \
--library L1522785992-trans transcriptome diseased True tutorial_data/L1522785992_trans.sorted.bam \
--convert breakdancer tutorial_data/breakdancer-1.4.5/*txt breakdancer \
--convert breakseq tutorial_data/breakseq-2.2/breakseq.vcf.gz breakseq \
--convert chimerascan tutorial_data/chimerascan-0.4.5/chimeras.bedpe chimerascan \
--convert defuse tutorial_data/defuse-0.6.2/results.classify.tsv defuse \
--convert manta tutorial_data/manta-1.0.0/diploidSV.vcf.gz tutorial_data/manta-1.0.0/somaticSV.vcf manta \
--assign L1522785992-trans chimerascan defuse \
--assign L1522785992-tumour breakdancer breakseq manta \
--assign L1522785992-normal breakdancer breakseq manta \
-w mavis.cfg
Setting Up the Pipeline
The next step is running the setup stage. This will perform conversion, clustering, and creating the submission scripts for the other stages.
mavis setup mavis.cfg -o output_dir/
At this stage you should have something that looks like this. For simplicity not all files/directories have been shown.
output_dir/
|-- build.cfg
|-- converted_inputs
| |-- breakdancer.tab
| |-- breakseq.tab
| |-- chimerascan.tab
| |-- defuse.tab
| `-- manta.tab
|-- L1522785992-normal_normal_genome
| |-- annotate
| | |-- batch-aUmErftiY7eEWvENfSeJwc-1/
| | `-- submit.sh
| |-- cluster
| | |-- batch-aUmErftiY7eEWvENfSeJwc-1.tab
| | |-- cluster_assignment.tab
| | |-- clusters.bed
| | |-- filtered_pairs.tab
| | `-- MAVIS-batch-aUmErftiY7eEWvENfSeJwc.COMPLETE
| `-- validate
| |-- batch-aUmErftiY7eEWvENfSeJwc-1/
| `-- submit.sh
|-- pairing
| `-- submit.sh
`-- summary
`-- submit.sh
Submitting Jobs to the Cluster
The last step is simple, ssh to your head node of your SLURM cluster (or run locally if you have configured remote_head_ssh and run the schedule step. This will submit the jobs and create the dependency chain
ssh head_node
mavis schedule -o output_dir --submit
The schedule step also acts as a built-in checker and can be run to check for errors or if the pipeline has completed.
mavis schedule -o output_dir
This should give you output something like below (times may vary) after your run completed correctly.
MAVIS: 2.0.0
hostname: gphost08.bcgsc.ca
[2018-06-02 19:47:56] arguments
command = 'schedule'
log = None
log_level = 'INFO'
output = 'output_dir/'
resubmit = False
submit = False
[2018-06-02 19:48:01] validate
MV_L1522785992-normal_batch-aUmErftiY7eEWvENfSeJwc (1701000) is COMPLETED
200 tasks are COMPLETED
run time: 609
MV_L1522785992-tumour_batch-aUmErftiY7eEWvENfSeJwc (1701001) is COMPLETED
200 tasks are COMPLETED
run time: 669
MV_L1522785992-trans_batch-aUmErftiY7eEWvENfSeJwc (1701002) is COMPLETED
23 tasks are COMPLETED
run time: 1307
[2018-06-02 19:48:02] annotate
MA_L1522785992-normal_batch-aUmErftiY7eEWvENfSeJwc (1701003) is COMPLETED
200 tasks are COMPLETED
run time: 622
MA_L1522785992-tumour_batch-aUmErftiY7eEWvENfSeJwc (1701004) is COMPLETED
200 tasks are COMPLETED
run time: 573
MA_L1522785992-trans_batch-aUmErftiY7eEWvENfSeJwc (1701005) is COMPLETED
23 tasks are COMPLETED
run time: 537
[2018-06-02 19:48:07] pairing
MP_batch-aUmErftiY7eEWvENfSeJwc (1701006) is COMPLETED
run time: 466
[2018-06-02 19:48:07] summary
MS_batch-aUmErftiY7eEWvENfSeJwc (1701007) is COMPLETED
run time: 465
parallel run time: 3545
rewriting: output_dir/build.cfg
run time (hh/mm/ss): 0:00:11
run time (s): 11
The parallel run time reported corresponds to the sum of the slowest job for each stage and does not include any queue time etc.
Analyzing the Output
The best place to start with looking at the MAVIS output is the summary folder which contains the final results. For column name definitions see the glossary.
output_dir/summary/mavis_summary_all_L1522785992-normal_L1522785992-trans_L1522785992-tumour.tab