modules/deepvariant_postprocessvariants

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

variant callingmachine learningneural network

https://github.com/nf-core/modules/[...]/modules/nf-core/deepvariant/postprocessvariants

Description

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`variant_calls_tfrecord_files`
`:file`

One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS

*.tfrecord.gz

`gvcf_tfrecords`
`:file`

Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output

*.gz

`small_model_calls`
`:file`

Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with variant calls from the small model

*.gz

`phase_inputs`
`:file`

Sharded phased read inputs tsv file from DEEPVARIANT_MAKEEXAMPLES

*.tsv

`intervals`
`:file`

Interval file for targeted regions

*.bed

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fai`
`:file`

Index of reference fasta file

*.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`gzi`
`:file`

GZI index of reference fasta file

*.gzi

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.vcf.gz`
`:file`

Compressed VCF file

*.vcf.gz

`vcf_index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.vcf.gz.{tbi,csi}`
`:file`

Index for VCF

$*.vcf.gz.{tbi,csi}

`gvcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.g.vcf.gz`
`:file`

Compressed GVCF file

*.g.vcf.gz

`gvcf_index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.g.vcf.gz.{tbi,csi}`
`:file`

Index for GVCF

*.g.vcf.gz.{tbi,csi}

`versions_deepvariant`

`${task.process}`
`:string`

The process the versions were collected from

`deepvariant`
`:string`

The tool name

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`deepvariant`
`:string`

The tool name

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

The expression to obtain the version of the tool

Tools

deepvariant
BSD-3-clause

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

github.com/google/deepvariant 10.1038/nbt.4235

modules/deepvariant_postprocessvariants

Description

Input

meta :map

variant_calls_tfrecord_files :file

gvcf_tfrecords :file

small_model_calls :file

phase_inputs :file

intervals :file

meta2 :map

fasta :file

meta3 :map

fai :file

meta4 :map

gzi :file

Output

vcf

meta :map

${prefix}.vcf.gz :file

vcf_index

meta :map

${prefix}.vcf.gz.{tbi,csi} :file

gvcf

meta :map

${prefix}.g.vcf.gz :file

gvcf_index

meta :map

${prefix}.g.vcf.gz.{tbi,csi} :file

versions_deepvariant

${task.process} :string

deepvariant :string

/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //' :eval

Topics

versions

${task.process} :string

deepvariant :string

/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //' :eval

Tools

deepvariantBSD-3-clause

included in

maintainers

get in touch

`meta`
`:map`

`variant_calls_tfrecord_files`
`:file`

`gvcf_tfrecords`
`:file`

`small_model_calls`
`:file`

`phase_inputs`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`vcf`

`meta`
`:map`

`${prefix}.vcf.gz`
`:file`

`vcf_index`

`meta`
`:map`

`${prefix}.vcf.gz.{tbi,csi}`
`:file`

`gvcf`

`meta`
`:map`

`${prefix}.g.vcf.gz`
`:file`

`gvcf_index`

`meta`
`:map`

`${prefix}.g.vcf.gz.{tbi,csi}`
`:file`

`versions_deepvariant`

`${task.process}`
`:string`

`deepvariant`
`:string`

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

`versions`

`${task.process}`
`:string`

`deepvariant`
`:string`

`/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'`
`:eval`

deepvariant
BSD-3-clause