Open Melalaoua opened 4 months ago
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)
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
{ "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": "" }
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" } } } } }
main latest (07266811ffc5772cbfab790e8da0c49cea7e7e08)
@JbaptisteLam
Not able to reproduce the error or it's already fixed in the release
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 (07266811ffc5772cbfab790e8da0c49cea7e7e08)
@JbaptisteLam