DeepVariant+GLnexus workflows
These portable WDL workflows use DeepVariant to call variants from WGS read alignments, followed by GLnexus to merge the resulting Genome VCF (gVCF) files for several samples into a Project VCF (pVCF). The wdl/ directory has three nested workflows:
DeepVariant.wdl
Based on the DeepVariant docs, the sequential workflow to generate gVCF from a given BAM file and genomic range.
+----------------------------------------------------------------------------+
| |
| DeepVariant.wdl |
| |
| +-----------------+ +-----------------+ +------------------------+ |
sample.bam | | | | | | | |
genome.fa -----> make_examples |----> call_variants |----> postprocess_variants |-----> gVCF
range | | | | | | | |
| +-----------------+ +--------^--------+ +------------------------+ |
| | |
| | |
+----------------------------------|-----------------------------------------+
|
DeepVariant Model
make_examples and call_variants internally parallelize across CPUs on the machine they run on. The tasks use the docker image published by the DeepVariant team.
htsget_DeepVariant.wdl
To further parallelize WGS calling accross several machines, scatters DeepVariant.wdl across several genomic ranges (typically full-length chromosomes). For each range, fetches a BAM slice using the GA4GH htsget client in samtools 1.7+, given an htsget server endpoint and sample ID. Finally, concatenates the per-range gVCFs to the complete product.
+--------------------------------------------------------------------------------+
| |
| htsget_DeepVariant.wdl |
| |
| +-----------------+ +-------------------+ |
| | | | | range gVCF |
| +---> htsget client |----> DeepVariant.wdl |---+ |
| | | (samtools) | | | | |
| | | | +-------------------+ | |
sample ID | | +-----------------+ | +-------------------+ |
| | +--> | |
ranges -------+---> ... ... ... ---> bcftools concat +-----> sample gVCF
(e.g. | | +--> | |
chr1 | | +-----------------+ | +-------------------+ |
chr2 | | | | +-------------------+ | |
...) | +---> htsget client | | | | |
| | (samtools) |----> DeepVariant.wdl |---+ |
| | | | | range gVCF |
| +------------^----+ +-------------------+ |
| | | |
| | | |
+------------|-------|-----------------------------------------------------------+
| |
sample ID | |
range | | range BAM
| |
+----v------------+
| |
| htsget server |
| |
+-----------------+
By using htsget, the workflow scatters across the ranges without first having to download and slice up a monolithic BAM file.
htsget_DeepVariant_GLnexus.wdl
Scatters htsget_DeepVariant.wdl across several samples to generate an array of gVCF files, then feeds these to GLnexus to merge them into a pVCF.
+-----------------------------------------------------------+
| |
| htsget_DeepVariant_GLnexus.wdl |
| |
| +--------------------------+ |
| | | sample gVCF |
| +---> htsget_DeepVariant.wdl |----+ |
| | | | | |
| | +--------------------------+ | +-----------+ |
| | +----> | |
sample IDs -------+---> ... ... -----> GLnexus +----> project VCF
| | +----> | |
| | +--------------------------+ | +-----------+ |
| | | | | |
| +---> htsget_DeepVariant.wdl |----+ |
| | | sample gVCF |
| +--------------------------+ |
| |
+-----------------------------------------------------------+
Here's an example inputs JSON providing everything required to launch this top-level workflow with dxWDL or Cromwell:
{
"htsget_DeepVariant_GLnexus.accessions": ["NA12878","NA12891","NA12892"],
"htsget_DeepVariant_GLnexus.htsget_endpoint": "https://htsnexus.rnd.dnanex.us/v1/reads/BroadHiSeqX_b37",
"htsget_DeepVariant_GLnexus.ranges": ["12:112204691-112247789","17:41196312-41277500"],
"htsget_DeepVariant_GLnexus.ref_fasta_gz": (REFERENCE GENOME FILE),
"htsget_DeepVariant_GLnexus.model_tar": (DEEPVARIANT MODEL FILES),
"htsget_DeepVariant_GLnexus.output_name": "b37_CEUtrio_ALDH2_BRCA1",
}
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