Add ZFPM2 to reduced penetrance list

[jemten]

As a user of the scout and the raredisease pipeline I would like to add ZFPM2 to the list of genes with reduced penetrance to allow for better matching of inheritance models.

original freshdesk ticket: https://scilifelab.freshdesk.com/a/tickets/1007112

Acceptance Criteria

• Add to https://github.com/Clinical-Genomics/reference-files/blob/master/nallo/annotation/grch38_reduced_penetrance_-v1.0-.tsv
• Add to https://github.com/Clinical-Genomics/reference-files/blob/master/rare-disease/gene_panel/grch37_cust003-cmms-red-pen_-2017-.tsv and preferably rename file
• Add to https://github.com/Clinical-Genomics/reference-files/blob/master/rare-disease/gene_panel/grch38_cust003-cmms-red-pen_-2017-.tsv, fix formatting and rename

Notes

• Additional information.
• Dependencies.
• Related user stories.

[jemten]

I might be wrong but it seems to me that we have supplied the list of reduced penetrance genes in the wrong format all these years. It looks like genmod just grabs the first element of the tsv file expecting it to be the gene symbol.

https://github.com/Clinical-Genomics/genmod/blob/daee976a46843951cd3bee416d4b3c84631c4d92/genmod/commands/annotate_models.py#L123-L132

Our reduced penetrance list on the other hand have this format

reference-files/nallo/annotation/grch38_reduced_penetrance_-v1.0-.tsv

Lines 1 to 10 in b7e9b9c

	#Chromosome Gene_start Gene_stop HGNC_symbol Protein_name Symptoms Biochemistry Imaging Disease_trivial_name Trivial_name_short Phenotypic_disease_model OMIM_morbid Gene_locus UniProt_id Ensembl_gene_id Ensemble_transcript_ID Reduced_penetrance Clinical_db_gene_annotation Disease_associated_transcript Ensembl_transcript_to_refseq_transcript Gene_description Genetic_disease_model
	chr8 27459756 27479883 CHRNA2 CHRNA2:610353>AD CHRNA2:118502 8p21.2 ENSG00000120903 CHRNA2 FullList,EP CHRNA2:NM_000742.3 CHRNA2:ENST00000240132>NM_001282455/XM_005273396|ENST00000407991>NM_000742/XM_005273397|ENST00000518712|ENST00000520208|ENST00000520600|ENST00000520650|ENST00000520933|ENST00000521921|ENST00000522008|ENST00000523529|ENST00000523695|ENST00000524096 CHRNA2:cholinergic_receptor__nicotinic__alpha_2_(neuronal)
	chr20 63343223 63378401 CHRNA4 CHRNA4:600513>AD|188890 CHRNA4:118504 20q13.33 ENSG00000101204 CHRNA4 FullList,EP CHRNA4:ENST00000370263>NM_000744/NM_001256573/XM_005260189/XM_005260191|ENST00000463705|ENST00000467563|ENST00000475033|ENST00000480012|ENST00000498043 CHRNA4:cholinergic_receptor__nicotinic__alpha_4_(neuronal)
	chr1 154567778 154580013 CHRNB2 CHRNB2:605375 CHRNB2:118507 1q21.3 ENSG00000160716 CHRNB2 FullList,EP CHRNB2:NM_000748.2 CHRNB2:ENST00000368476>NM_000748 CHRNB2:cholinergic_receptor__nicotinic__beta_2_(neuronal)
	chr15 45114326 45118421 DUOXA2 DUOXA2:274900>AR DUOXA2:612772 15q21.1 ENSG00000140274 DUOXA2 FullList,IEM DUOXA2:NM_207581 DUOXA2:ENST00000323030>NM_207581|ENST00000350243|ENST00000491993 DUOXA2:dual_oxidase_maturation_factor_2
	chr14 36516392 36521149 NKX2-1 NKX2-1:610978>AD|118700>AD|188550 NKX2-1:600635 14q13.3 ENSG00000136352 NKX2-1 FullList,IEM NKX2-1:NM_001079668 NKX2-1:ENST00000354822>NM_001079668/XM_005268030/XM_005268031/XM_005268032/XM_005268033|ENST00000498187>NM_003317|ENST00000518149|ENST00000522719|ENST00000546983 NKX2-1:NK2_homeobox_1
	chr2 165984641 166182806 SCN1A SCN1A:607208>AD|609634>AD|604403>AD SCN1A:182389 2q24.3 ENSG00000144285 SCN1A FullList,EP SCN1A:NM_001165963.1 SCN1A:ENST00000303395|ENST00000375405>NM_001165964/NM_006920|ENST00000409050|ENST00000423058>NM_001165963/NM_001202435|ENST00000473295|ENST00000491429|ENST00000507401 SCN1A:sodium_channel__voltage-gated__type_I__alpha_subunit
	chr19 35030470 35040449 SCN1B SCN1B:615377>AD|612838|604233>AD SCN1B:600235 19q13.12 ENSG00000105711 SCN1B FullList,EP SCN1B:NM_001037.4 SCN1B:ENST00000262631>NM_001037/XM_005259144|ENST00000415950>NM_199037|ENST00000595652|ENST00000596348|ENST00000602150 SCN1B:sodium_channel__voltage-gated__type_I__beta_subunit
	chr1 112911847 112957593 SLC16A1 SLC16A1:245340>AD|610021>AD|616095>AR/AD SLC16A1:600682 1p13.2 ENSG00000155380 SLC16A1 FullList,IEM SLC16A1:NM_003051 SLC16A1:ENST00000369626>NM_003051/XM_005271150|ENST00000429288|ENST00000433570|ENST00000443580|ENST00000458229|ENST00000478835|ENST00000481750|ENST00000538576>NM_001166496 SLC16A1:solute_carrier_family_16_(monocarboxylate_transporter)__member_1
	chrX 56563627 56567868 UBQLN2 UBQLN2:300857>XD UBQLN2:300264 Xp11.21 ENSG00000188021 UBQLN2 FullList,IEM UBQLN2:NM_013444 UBQLN2:ENST00000338222>NM_013444 UBQLN2:ubiquilin_2

Will test with just a simpel list of gene symbols

Edit: The genmod test fixture for this also suggests a single column gene symbol format
https://github.com/Clinical-Genomics/genmod/blob/daee976a46843951cd3bee416d4b3c84631c4d92/tests/fixtures/reduced_penetrance.tsv#L1-L2

[jemten]

Fixed in #138