This repository contains modified code of Ultima Genomics efficient_dv workflow (). This workflow runs on Ultima NGS data and is capable of calling small variants (SNVs) in either germline or somatic modes. Please consider this repository as a work in progress project as not all of it's elements have been thoroughly tested in production environment.
The diagram below outlines the connections between tasks and resource modules with outputs specific to each of two modes listed in a table, also see below
| Output | Type | Description |
|---|---|---|
nvidia_smi_log |
File | nvidia GPU run log |
output_vcf |
File | vcf file with calls, either germline or somatic |
output_vcf_index |
File | index of the output vcf file |
vcf_no_ref_calls |
File | output vcf file with reference calls removed |
vcf_no_ref_calls_index |
File | = RemoveRefCalls.output_vcf_index |
output_gvcf |
File? | Optional GVCF file |
output_gvcf_index |
File? | Optional index of GVCF file |
output_gvcf_hcr |
File? | Optional HCR file for GVCF |
realigned_cram |
File? | Optional realigned CRAM file |
realigned_cram_index |
File? | Optional index of realigned CRAM |
report_html |
File | QC report file, HTML |
qc_h5 |
File | QC report output, h5 file |
qc_metrics_h5 |
File | QC report output, metrics h5 file |
Efficient DV uses multiple resources which may be downloaded from Ultima Genomics website(s) and Amazon buckets. A simple bash script is included, although in the nearest future we may switch to using efficient_dv resources wrapped in modules (with Modulator).