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nf-core/deepsomatic @ 0.0.0-0c7146d

DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.

variant calling machine learning neural network
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @vaxyzek
Maintainers: @vaxyzek

Summary

DeepSomatic is an extension of deep learning-based variant caller DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and normal data, produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports somatic variants in a standard VCF or gVCF file.

Get started

Add the following snippet to your workflow script to include this module.

include { DEEPSOMATIC } from 'nf-core/deepsomatic'

License

MIT License

Process
Name DEEPSOMATIC
Input 5 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
input_normal file

BAM/CRAM file

 *.bam/cram
index_normal file

Index of BAM/CRAM file

 *.bai/crai
input_tumor file

BAM/CRAM file

 *.bam/cram
index_tumor file

Index of BAM/CRAM file

 *.bai/crai
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
intervals file

file containing intervals
#3 tuple
meta3 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
fasta file

The reference fasta file

 *.fasta
#4 tuple
meta4 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
fai file

Index of reference fasta file

 *.fai
#5 tuple
meta5 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
gzi file

GZI index of reference fasta file

 *.gzi
Output 5 channels
#1 vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}.vcf.gz file

Compressed VCF file

 *.vcf.gz
#2 gvcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}.g.vcf.gz file

Compressed GVCF file

 *.g.vcf.gz
#3 vcf_tbi tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}.vcf.gz.tbi file

Index of compressed VCF file

 *.vcf.gz.tbi
#4 gvcf_tbi tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}.g.vcf.gz.tbi file

Index of compressed Genotyped VCF file

 *.g.vcf.gz.tbi
#5 versions_deepsomatic tuple
${task.process} string

The name of the process
deepsomatic string

The name of the tool
1.7.0 eval

The expression to obtain the version of the tool
Tool Description Homepage
deepsomatic https://github.com/google/deepsomatic
Version 0.0.0-0c7146d