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5% frequency threshold for mitochondrial clinical vcfs #616

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merged 6 commits into from
Sep 25, 2024
Merged

5% frequency threshold for mitochondrial clinical vcfs #616

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ramprasadn Sep 24, 2024
eb963ec
Merge branch 'dev' of github.com:nf-core/raredisease into bcftools-fi…
ramprasadn Sep 24, 2024
c1ddf4c
changelog
ramprasadn Sep 24, 2024
7d5e14e
fix declaration error
ramprasadn Sep 24, 2024
69eb6a1
update docs
ramprasadn Sep 24, 2024
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lint
ramprasadn Sep 24, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- Report only variants above 5% heteroplasmy in the clinical vcf file for mitochondria [#616](https://github.com/nf-core/raredisease/pull/616)

### `Fixed`

### Parameters
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8 changes: 7 additions & 1 deletion conf/modules/generate_clinical_set.config
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Expand Up @@ -50,10 +50,16 @@ process {
process {
withName: '.*:GENERATE_CLINICAL_SET_MT:ENSEMBLVEP_FILTERVEP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
ext.prefix = { "${meta.id}_mt_filtervep_${meta.set}" }
ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" }
}

withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_FILTER' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
ext.args = { "-Oz -i 'AF>0.05'" }
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Could be good to add a line in the documentation saying that the default is not to output variants with a VAF below 5%.

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Done! 👍🏻

}

withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIP' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
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15 changes: 12 additions & 3 deletions subworkflows/local/generate_clinical_set.nf
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Expand Up @@ -5,11 +5,13 @@
include { ENSEMBLVEP_FILTERVEP } from '../../modules/nf-core/ensemblvep/filtervep'
include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip'
include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix'
include { BCFTOOLS_FILTER } from '../../modules/nf-core/bcftools/filter'

workflow GENERATE_CLINICAL_SET {
take:
ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ]
ch_hgnc_ids // channel: [mandatory] [ val(hgnc_ids) ]
val_ismt // value: if mitochondria, set to true

main:
ch_versions = Channel.empty()
Expand All @@ -28,16 +30,23 @@ workflow GENERATE_CLINICAL_SET {
.output
.set { ch_filtervep_out }

TABIX_BGZIP( ch_filtervep_out )
if (val_ismt) {
BCFTOOLS_FILTER (ch_filtervep_out)
ch_clinical = BCFTOOLS_FILTER.out.vcf
ch_versions = ch_versions.mix( BCFTOOLS_FILTER.out.versions )
} else {
TABIX_BGZIP( ch_filtervep_out )
ch_clinical = TABIX_BGZIP.out.output
ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions )
}

ch_clin_research_vcf.research
.mix( TABIX_BGZIP.out.output )
.mix( ch_clinical )
.set { ch_clin_research_split }

TABIX_TABIX( ch_clin_research_split )

ch_versions = ch_versions.mix( ENSEMBLVEP_FILTERVEP.out.versions )
ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions )
ch_versions = ch_versions.mix( TABIX_TABIX.out.versions )

emit:
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12 changes: 8 additions & 4 deletions workflows/raredisease.nf
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Expand Up @@ -550,7 +550,8 @@ workflow RAREDISEASE {

GENERATE_CLINICAL_SET_SNV(
ch_snv_annotate.vcf_ann,
ch_hgnc_ids
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions)

Expand Down Expand Up @@ -602,7 +603,8 @@ workflow RAREDISEASE {

GENERATE_CLINICAL_SET_MT(
ch_mt_annotate.vcf_ann,
ch_hgnc_ids
ch_hgnc_ids,
true
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions)

Expand Down Expand Up @@ -677,7 +679,8 @@ workflow RAREDISEASE {

GENERATE_CLINICAL_SET_SV(
ch_sv_annotate.vcf_ann,
ch_hgnc_ids
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SV.out.versions)

Expand Down Expand Up @@ -738,7 +741,8 @@ workflow RAREDISEASE {

GENERATE_CLINICAL_SET_ME(
ANNOTATE_MOBILE_ELEMENTS.out.vcf,
ch_hgnc_ids
ch_hgnc_ids,
false
)
ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_ME.out.versions )

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