Running AIM

Running AIM#

Quick Start#

AIM

Install the software and data dependencies. Download our example here.

docker run -u $(id -u):$(id -g) \
        -v <Path to VCF File>:/input/vcf.gz \
        -v <Path to HPO file>:/input/hpo.txt \
        -v <Path to downloaded database>:/run/data_dependencies \
        -v <Path to output folder>:/out \
    chaozhongliu/aim-lite /run/proc.sh [Sample ID] [Reference genome: hg19/hg38] [Memory Limit (G)]

Arguments Explanation#

AIM arguments#

Argument

Explanation

Path to VCF File

Full path to the sample VCF. See Input Data Preparation for details

Path to HPO file

Full path to HPO list, formatted as txt, each row is an HPO term.

Path to downloaded database

Full path to data dependencies downloaded

Path to output folder

Full path to output folder, must already exist

Sample ID

Can be any ID. It’s used as output frefix

Reference genome

Reference genome used to map reads and call variants. AIM support hg19 and hg38

Memory Limit

The maximum memory allocated to AIM. If the system has 48G RAM, 32 to 36 as recommended
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