#!/bin/bash -Ceuo pipefail
annotateFusionVcf.py \
    --vcf 1173_KQG-T1-TDNA-01_A23T3TCLT4_1_vs_1173_KQG-N1-BDNA-01_A23KFG7LT4_1.manta_fusion.somatic_sv.vcf.gz \
    --genes protein_coding_genes.bed \
    --actionable-bed foresight_panel_for_manta.bed \
    --out 1173_KQG-T1-TDNA-01_A23T3TCLT4_1_vs_1173_KQG-N1-BDNA-01_A23KFG7LT4_1.manta_fusion.somatic_sv.annotated.vcf

bgzip  1173_KQG-T1-TDNA-01_A23T3TCLT4_1_vs_1173_KQG-N1-BDNA-01_A23KFG7LT4_1.manta_fusion.somatic_sv.annotated.vcf
tabix -p vcf 1173_KQG-T1-TDNA-01_A23T3TCLT4_1_vs_1173_KQG-N1-BDNA-01_A23KFG7LT4_1.manta_fusion.somatic_sv.annotated.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE":
    python: $( python3 --version 2>&1 | sed 's/Python //' )
    annotateFusionVcf: "1.0.0"
END_VERSIONS