This workflow will run the SvABA structural variation (SV) analysis for a set of tumor-normal pairs, starting from the aligned BAM files. The analysis includes structural variant prediction and and determine SV classes. SV classes are predicted by combining SV results with copy number results previously generated by TitanCNA.
Gavin Ha
Fred Hutchinson Cancer Research Center
contact: gavinha@gmail.com or gha@fredhutch.org
Date: May 15, 2019
- R-3.4
-optparse
-data.table
-GenomicRanges
-GenomeInfoDb
-VariantAnnotation
-plyr
-ggplot2
-reshape2
-stringr - Python 3.4
- snakemake-5.4
- samtools-1.3.1
The list of tumour-normal paired samples should be defined in a YAML file. See config/samples.yaml
for an example. Both fields samples
and pairings
must to be provided. pairings
key must match the tumour sample while the value must match the normal sample.
samples:
tumor_sample_1: /path/to/bam/tumor.bam
normal_sample_1: /path/to/bam/normal.bam
pairings:
tumor_sample_1: normal_sample_1
The first snakemake file svaba.snakefile will a. Run the full SvABA analysis
# show commands and workflow
snakemake -s svaba.snakefile -np
# run the workflow locally using 5 cores
snakemake -s svaba.snakefile --cores 5
2. Integrating SV and copy number results (TitanCNA)
The second snakemake file combineSvabaTitan.snakefile will a. Combine SvABA and TitanCNA results to assign copy number to the breakpoints and rearrangement classes to the SV events. b. Plot copy number and SV for each chromosome.
snakemake -s combineSvabaTitan.snakefile --cores 5
The third snakemake file plotSVandCNAzoom.snakefile generates custom plots zoomed in for a region of interest. Users can specify the coordinates in the configPlotZoom.yaml file. See the description of the configuration below.
snakemake -s plotSVandCNAzoom.snakefile --cores 5
If you are using a cluster, then these are resource settings for memory and runtime limits, and parallel environments.
These are the default settings for all tasks that do not have rule-specific resources.
There are two cluster configurations provided: qsub
and slurm
There are 2 separate files in use for qsub
, which are provided as a template:
config/cluster_qsub.sh
- This file contains other qsub
parameters. Note that these settings are used for the Broad's UGER cluster so users will need to modify this for their own clusters.
config/cluster_qsub.yaml
- This file contains the memory, runtime, and number of cores for certain tasks.
To invoke the snakemake pipeline for qsub
:
snakemake -s svaba.snakefile --jobscript config/cluster_qsub.sh --cluster-config config/cluster_qsub.yaml --cluster-sync "qsub -l h_vmem={cluster.h_vmem},h_rt={cluster.h_rt} -pe {cluster.pe} -binding {cluster.binding}" -j 100
Here, the h_vmem
(max memory), h_rt
(max runtime) are used. For runSvaba
task, the default setting is to use 4 cores and this can be set with -pe
and -binding
. Your SGE settings may be different and users should adjust accordingly.
There is only one file in use for slurm
:
config/cluster_slurm.yaml
- This file contains the memory, runtime, and number of cores for certain tasks.
To invoke the snakemake pipeline for slurm
:
snakemake -s svaba.snakefile --cluster-config config/cluster_slurm.yaml --cluster "sbatch -p {cluster.partition} --mem={cluster.mem} -t {cluster.time} -c {cluster.ncpus} -n {cluster.ntasks} -o {cluster.output}" -j 50
All settings for the workflow are contained in config/config.yaml. The settings are organized by paths to scripts and reference files and then by each step in the workflow.
svaba_exe
is the compiled SvABA executable
svaba_exe: /path/to/svaba
samTools: /path/to/samtools
These are provided in this repo under code/.
svaba_funcs: code/svaba_utils.R
plot_funcs: code/plotting.R
combineSVCN_script: code/combineSVABAandTITAN.R
plotSVCN_script: code/plotTitanSvaba.R
Specify the directory in which TitanCNA are installed.
Set these if the R files in these libraries have been modified or updated but not yet installed or updated in R.
titan_libdir: /path/to/TitanCNA/
Specifies the TitanCNA snakemake location containing result files to be merged with SvABA results in combineSvabaTitan.snakefile.
titan_results: /path/to/TitanCNA/snakemake_results/
Global reference files used by the snakefiles
and scripts.
refGenome
specify the reference genome used for aligning the sequenced readsgenomeStyle
specifies the chromosome naming convention to used for output files. Input files can be any convention as long as it is the same genome build. Only useUCSC
(e.g. chr1) orNCBI
(e.g. 1).cytobandFile
is used for plotting the chromosome idiograms and only needs to specify data/cytoBand_hg38.txt if using hg38.chrs
specifies the chromosomes to analyze; users do not need to be concerned about chromosome naming convention here as the code will handle it based on thegenomeStyle
.
refGenome: /path/to/ref/genome.fasta
genomeBuild: hg38
genomeStyle: UCSC
cytobandFile: data/cytoBand_hg38.txt # only need if hg38
chrs: c(1:22, \"X\")
6. svaba.snakefile settings: SvABA
svaba_dbSNPindelVCF
specifies a VCF file containing known indels to use for germline filtering Homo_sapiens_assembly38.known_indels.vcf.gz
svaba_dbSNPindelVCF: /path/to/dbsnp_indel.vcf
svaba_numThreads: 4 # should match cluster settings for number of cores
7. combineSvabaTitan.snakefile settings: Plotting
Settings used for plotting copy number and SV results for all chromosomes. Note that this differs from the custom user zoom plots using plotSVandCNAzoom.snakefile.
plot_geneFile
is a text file listing the regions to annotate in the plot. 4 column file: name, chr, start, stop.
plot_zoom: FALSE
plot_chrs: c(1:22, \"X\") # "None" will also plot all chromosomes
plot_startPos: None
plot_endPos: None
plot_geneFile: data/AR_coord.txt ## include list of genes to annotate on plot
plot_ylim: c(-2,6)
plot_size: c(8,4)
plot_type: titan ## titan - will include haplotype fraction
plot_format: png
8. plotSVandCNAzoom.snakefile settings in configPlotZoom.yaml
plot_id
to use for naming the output directory containing the zoomed plots for each sample.plot_zoom
indicates the plot should be focused on a specific region smaller than a whole chromosome. If set toTRUE
, thenplot_chrs
(should only be a single chr),plot_startPos
,plot_endPos
should be set.- 'plot_type
is set to
ichorfor total copy number only (black dots). Set it to
titan` to also include the allelic fraction panel as a second track.
plot_id: AR_enhancer_zoom
plot_zoom: TRUE
plot_chrs: c(\"X\")
plot_startPos: 66500000
plot_endPos: 67900000
plot_geneFile: data/AR_coord.txt ## include list of genes to annotate on plot
plot_ylim: c(-2,6)
plot_size: c(8,4)
plot_type: ichor ## use "titan" to also plot the allelic fraction panel
plot_format: png