Setting | Description |
|---|---|
Load dictionary or load NCBI XML | You must load one of the following three dictionary files, where XML is the preferred format. • Human - NCBI XML file for alleles. You can download an NCBI XML for human alleles from the ncbi database—ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/alleles/. • Non-human primate - EBI XML or FASTA file for alleles. You can download an XML or FASTA file for non-human primate alleles from the MHC/NHP database—ftp://fftp.ebi.ac.uk/pub/databases/ipd/mhc/nhp/. • HLA Dictionary .fasta file. You can download the HLA dictionary sequences from the IMGT/HLA database—http://www.ebi.ac.uk/imgt/hla/. |
Coverage Threshold - The coverage requirements to call alleles that are present in the sample data. | |
Minimum Coverage | The minimum number of reads that must cover an allele. |
Percent coverage | The percentage of the gene that must be covered by reads for the allele to be called in the gene. You should set this value based on the region that is being targeted. For example, if you are targeting just exons, then this value should be less than 50%. (An acceptable value is 10%.) If you are targeting the whole gene, then this value should be greater than 50%. (An acceptable value is 90%.) |
Minimum read length | Any read that does not meet or exceed the indicated threshold is not used for calling alleles. |
Align each sample file to only reference file | Select this option if you load a separate sample file for each gene that is being targeted. |
Mutation filter | |
Check reads balance when mutation percentage < 20%. | Selected by default. If the frequency of a variant is less than 20%, then the Read Balance is checked. If the reads for the variant are not balanced, then the variant is ignored and it is not used for allele calling. |