damiansm
commented
1 year ago Hi,
You need to prepare a tab-delimited file with the chromosome, position, ref, alt and percentage allele frequency, make sure it is sorted by chromosome and position and then create a tabix index of it. If you then specify the path to it in application.properties and state LOCAL as a frequency source in the yml configs
Best wishes Damian
On Thu, Feb 2, 2023 at 9:21 PM patrickrshea @.***> wrote:
I am trying to add a local variant frequency database to perform MAF filtering in Exomiser. In response to my question on the Discussion page about blacklisting variants, I was advised to create a list of variant frequencies and point application.properties to the file path and set LOCAL in the list of frequency databases. Can the format for this file be a simple tab-delimited text file with VariantID and MAF or does it have to be in some sort of database format? I looked through the documentation and did not find any information on the specifications for this file format and the hg19_variants.mv.db file, which I believe contains the files for the 1KG and gnomAD MAFs, appears to be in some type of database format. However I can't tell exactly which one.
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patrickrshea
I am trying to add a local variant frequency database to perform MAF filtering in Exomiser. In response to my question on the Discussion page about blacklisting variants, I was advised to create a list of variant frequencies and point application.properties to the file path and set LOCAL in the list of frequency databases. Can the format for this file be a simple tab-delimited text file with VariantID and MAF or does it have to be in some sort of database format? I looked through the documentation and did not find any information on the specifications for this file format and the hg19_variants.mv.db file, which I believe contains the files for the 1KG and gnomAD MAFs, appears to be in some type of database format. However I can't tell exactly which one.