Input Data Preparation

Input Data Preparation#

Input VCF file#

AIM accepts most of the variant calling VCF output. Please see below the checklist before running the software.

  1. The VCF file must contain FILTER column with PASS flag

  2. The VCF should not contain any unknown chromosomes (future version of AIM plans to handle this automatically)

  3. Both hg19 and hg38 referene genomes are acceptable.

  4. The VCF file must be compressed using bgzip

Input HPO file#

AIM accepts phenotype information as a list of HPO (Human Phenotype Ontology) terms.

Here is an example file called hpos.txt:

HP:0000365
HP:0000508
HP:0001249
HP:0001263
HP:0001999

If you only have clinical notes in hand, please try our AI-MARRVEL website to convert it into HPO terms.

Note

We are packaging this clinical notes to HPO terms step into AIM pipeline.

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