nf-core/deepvariant
Please consider using/contributing to https://github.com/nf-core/sarek
deep-variantdnagooglevariant-calling
This pipeline uses DSL1. It will not work with Nextflow versions after
Launch version 1.0 https://github.com/nf-core/deepvariant 22.10.6
.
Learn more.
Output
This document describes the processes and output produced by the pipeline.
Main steps:
-
preprocessing of fasta/reference files (fai, fastagz, gzfai & gzi)
- These steps can be skipped if the the
--genome
options is used or the fai, fastagz, gzfai & gzi files are supplied.
- These steps can be skipped if the the
-
preprocessing of BAM files
- Also can be skipped if BAM files contain necessary read group line
-
make examples
- Gets bam files and converts them to images ( named examples )
-
call variants
- Does the variant calling based on the ML trained model.
-
post processing
- Trasforms the variant calling output (tfrecord file) into a standard vcf file.
For further reading and documentation about deepvariant see google/deepvariant
VCF
The output from DeepVariant is a variant call file or vcf v4.2
Output directory: results
(by default)
pipeline_info
- produced by nextflow
{bamSampleName}.vcf
- output vcf file produced by deepvariant