Omim annotation issue : gene list not sorted

[Melalaoua]

Issue

Tabix throw error that omim bed file generated from howard is not sorted (likely gene on negative strand are not correctly inserted in the bed file)

Omim bed annotation creation

howard databases --input_extann path/to/extann --output_extann OMIMannota
tion.bed --refgene path/to/refseq.bed --genomes-folder /path/to/genome/folder --genome path/to/genome.fasta --param_extann path/to/extann_param.json

Extann file :

{
"OMIMannotations": {
"reference": "hg19",
"genes": {
"Number": "1",
"Type": "String",
"Description": "Gene symbol"
},
"transcript": {
"Number": "1",
"Type": "String",
"Description": "Refgene transcript"
},
"OMIM_phenotype": {
"Number": ".",
"Type": "String",
"Description": "List of OMIM phenotype"
},
"OMIM_inheritance": {
"Number": ".",
"Type": "String",
"Description": "List of OMIM inheritance"
},
"OMIM_ID": {
"Number": ".",
"Type": "Integer",
"Description": "List of OMIM ID"
}
},
"replace": {
",": "|",
";": ","
},
"extra_col_list": [
"transcript"
],
"transcript_extann": "",
"mode_extann": "",
"refgene_extann": ""
}

For what use ?

To howard process a vcf with omim annotation
howard process --input=test.vcf --output=output.vcf --param=param.json

Param.json file :
{
"annotation": {
"bcftools" : {
"annotations" : {
"/databases/OMIMannotations/current/hg19/sorted_OMIMannotation.all.bed.gz": {
"OMIM_phenotype": "OMIM_phenotype",
"OMIM_ID": "OMIM_ID",
"OMIM_inheritance" : "OMIM_inheritance"
}
}
}
}
}

Howard version ?

main latest (0726681)

@JbaptisteLam

[JbaptisteLam]

Not able to reproduce the error or it's already fixed in the release