Merge branch 'CW-3773-chrM' into 'dev'

ChrM annotations [CW-3773]

Closes CW-3773

See merge request epi2melabs/workflows/wf-human-variation!299

CHANGELOG.md

@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [unreleased]
+### Fixed
+- ERROR_OUT_OF_CHROMOSOME_RANGE annotation in VCF on `chrM` variants due to different nomenclature used by SnpEff.
 ### Changed
 - Reconciled workflow with wf-template v5.2.0
 - Removed `FXN` homopolymer region from list of STRs genotyped by `--str` sub-workflow

modules/local/common.nf

@@ -430,7 +430,9 @@ process annotate_vcf {
     else
         # SNP is slow to annotate, we'll break it apart by contig
         # and merge it back later. filter the master VCF to current contig
-        bcftools view -r !{contig} input.vcf.gz | bgzip > input.chr.vcf.gz
+        # Also, relabel chrM as chrMT so SnpEff can annotate
+        bcftools view -r !{contig} input.vcf.gz | sed 's/^chrM\\t/chrMT\\t/' | bgzip > input.chr.vcf.gz
+
         INPUT_FILENAME=input.chr.vcf.gz
         OUTPUT_LABEL="!{output_label}.!{contig}"
     fi
@@ -451,7 +453,9 @@ process annotate_vcf {
             clinvar_vcf="${CLINVAR_PATH}/clinvar_GRCh37.vcf.gz"
         fi
 
-        snpEff -Xmx!{task.memory.giga - 1}g ann -noStats -noLog $snpeff_db ${INPUT_FILENAME} > !{params.sample_name}.intermediate.snpeff_annotated.vcf
+        # Revert back chrMT to chrM
+        snpEff -Xmx!{task.memory.giga - 1}g ann -noStats -noLog $snpeff_db ${INPUT_FILENAME} | sed 's/^chrMT\\t/chrM\\t/' > !{params.sample_name}.intermediate.snpeff_annotated.vcf
+
         # Add ClinVar annotations
         SnpSift annotate $clinvar_vcf !{params.sample_name}.intermediate.snpeff_annotated.vcf | bgzip > !{params.sample_name}.wf_${OUTPUT_LABEL}.vcf.gz
         tabix !{params.sample_name}.wf_${OUTPUT_LABEL}.vcf.gz