somatic-variant-caller

An example run of the pipeline may look something like this:

nextflow run lifebit-ai/somatic-variant-caller --genome hg19 --samples s3://lifebit-featured-datasets/pipelines/gatk-somatic-data/samples.tsv --bed s3://lifebit-featured-datasets/pipelines/DeepVariant/quick_test/test_nist.b37_chr20_100kbp_at_10mb.bed

Dependencies

Nextflow Docker

Deploit

The pipeline can also be run on Deploit, a bioinformatics platform to help you run your analysis over the cloud which is free for indiviudal users

See an example job run on the Deploit platform here