modules/deepvariant_makeexamples

Transforms the input alignments to a format suitable for the deep neural network variant caller

variant callingmachine learningneural network

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

Description

Transforms the input alignments to a format suitable for the deep neural network variant caller

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM file

*.bam/cram

`index`
`:file`

Index of BAM/CRAM file

*.bai/crai

`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

`meta5`
`:map`

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

*.gzi

`par_bed`
`:file`

BED file containing PAR regions

*.bed

Output

name:type

description

pattern

`examples`

`meta`
`:list`

Tuple containing sample metadata and examples that can be used for calling

`${prefix}.examples.tfrecord--of-.gz{,.example_info.json}`
`:list`

Tuple containing sample metadata and examples that can be used for calling

`gvcf`

`meta`
`:list`

Tuple containing sample metadata and examples that can be used for calling

`${prefix}.gvcf.tfrecord--of-.gz`
`:list`

Tuple containing sample metadata and the GVCF data in tfrecord format

`small_model_calls`

`meta`
`:list`

Tuple containing sample metadata and examples that can be used for calling

`${prefix}_call_variant_outputs.examples.tfrecord--of-.gz`
`:list`

Optional variant calls from the small model, if enabled, in tfrecord format

`versions`

`versions.yml`
`:file`

File containing the DeepVariant software version

versions.yml

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_makeexamples

Description

Input

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`meta5`
`:map`

`par_bed`
`:file`

Output

`examples`

`meta`
`:list`

`${prefix}.examples.tfrecord--of-.gz{,.example_info.json}`
`:list`

`gvcf`

`meta`
`:list`

`${prefix}.gvcf.tfrecord--of-.gz`
`:list`

`small_model_calls`

`meta`
`:list`

`${prefix}_call_variant_outputs.examples.tfrecord--of-.gz`
`:list`

`versions`

`versions.yml`
`:file`

Tools

deepvariant
BSD-3-clause

included in

maintainers

get in touch

modules/deepvariant_makeexamples

Description

Input

meta:map

input:file

index:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

gzi:file

meta5:map

par_bed:file

Output

examples

meta:list

${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}:list

gvcf

meta:list

${prefix}.gvcf.tfrecord-*-of-*.gz:list

small_model_calls

meta:list

${prefix}_call_variant_outputs.examples.tfrecord-*-of-*.gz:list

versions

versions.yml:file

Tools

deepvariant BSD-3-clause

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`meta5`
`:map`

`par_bed`
`:file`

`examples`

`meta`
`:list`

`${prefix}.examples.tfrecord--of-.gz{,.example_info.json}`
`:list`

`gvcf`

`meta`
`:list`

`${prefix}.gvcf.tfrecord--of-.gz`
`:list`

`small_model_calls`

`meta`
`:list`

`${prefix}_call_variant_outputs.examples.tfrecord--of-.gz`
`:list`

`versions`

`versions.yml`
`:file`

deepvariant
BSD-3-clause