Dx wrapper to run the GATK germlineCNVcaller and generate per sample gCNV.bed file for copy ratio visualisation and summarise CNV calls across samples on a run. This is the source code for an app that runs on the DNAnexus Platform.
Calls copy number variants (CNV) from a minimum of 30 samples based on variation in read depth of exome sequencing data.
Generates a gCNV.bed file for the visualisation of CNV calls in IGV.js.
This app may be executed as standalone or as part of an analysis pipeline.
Input files (preprocessed and annotated target intervals) come from the GATKgCNV_prep app and input bam and bai files come from the Sentieon app of the NGS data processing workflow (eg Dias single).
This app requires:
- at least 30 pairs of sample.bam and sample.bai files from the same sequencing run (-ibambis array of files)
- preprocessed.interval_list specifying the intervals where CNVs should be called (-iinterval_list)
- a corresponding annotation.tsv that has GC content and optionally other information about each of the target intervals (-iannotation_tsv)
- OPTIONAL to provide a prior probability.tsv for CNV calling (app has a built-in default)
Parameters to calculate coverage, filter out low quality intervals and call variants:
- low read depth threshold - discard intervals with low coverage across the majority of samples
- low percentage threshold - if interval is covered below threshold in samples above this percentage then filter out that interval
- minimum and maxinmum GC content of interval
- minimum and maximum mappability of interval - depending if annotation.tsv has this information
- (minimum and maximum segmental duplication of interval) - depending on whether annotation.tsv has this information
- a pair of _intervals.vcf (genotype of every interval in the input bed) and _segments.vcf (consecutive intervals with the same CNV status are merged) for each sample
- gCNV.bed files for copy ratio visualisation in IGV.js for each sample
- a gCNV.bed file of all samples on the run
- list of intervals excluded from CNV calling for the run, a 0-based BED file
How to run this app:
dx run app-eggd_GATKgCNV_call/1.0.0 \
-iGATK_docker="<GATK_docker.tar.gz>" \
-iinterval_list="<output from prep app>" \
-iannotation_tsv="<output from prep app>" \
-ibambais="<array of paired sample bam and index file IDs>"The app requires a tar.gz of the Docker image for GATK 4.2+ as an input. Htslib and bedtools are bundled with the app. Deb files for parallel and its dependency sysstat are bundled with the app in resources/home/dnanexus/.