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.

• 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