genomestudio

A few methods of using Illumina's Genome Studio for genotype calling

Run with docker

docker image can be built as follows

cd docker
docker build --tag genomestudio .

Now with docker image, run on local idats, cluster, and manifest files

docker run --rm -v <local data dir>:/mnt genomestudio /home/iaap-cli-linux-x64-1.1.0-sha.80d7e5b3d9c1fdfc2e99b472a90652fd3848bbc7/iaap-cli/iaap-cli gencall /mnt/Manifest_cluster_files/GSA-24v3-0_A2.bpm /mnt/Manifest_cluster_files/GSA-24v3-0_A1_ClusterFile.egt /mnt/output -f /mnt/204118120034/ -p

where <local data dir> is a local directory containing all idats, cluster and manifest files.

gencall works as follows:

/home/iaap-cli-linux-x64-1.1.0-sha.80d7e5b3d9c1fdfc2e99b472a90652fd3848bbc7/iaap-cli/iaap-cli gencall <manifest (.bpm)> <clusterfile (.egt)> <output dir> -f <path/to/idats/> -p

-p to make .ped output used in this run. (use -g to make .gtc output)

--rm removes container after run is complete

-v creates a volume with local dir mounted to /mnt in docker container (I chose to mount volume to /mnt but you could do this in any dir inside the container that you like).

Docker Example

docker run --rm -v /Users/vitaled2/Desktop/genome_studio/ilmnTestData:/mnt genomestudio /home/iaap-cli-linux-x64-1.1.0-sha.80d7e5b3d9c1fdfc2e99b472a90652fd3848bbc7/iaap-cli/iaap-cli gencall /mnt/Manifest_cluster_files/GSA-24v3-0_A2.bpm /mnt/Manifest_cluster_files/GSA-24v3-0_A1_ClusterFile.egt /mnt/output -f /mnt/204118120034/ -p

Local Genome Studio CLI Parallel processing python script

This parallelizes runs for different sets of idats with same cluster/manifest

Run like this:

python3 genome_studio_multi_caller.py --idats /data/vitaled2/genomestudio/idat_paths.txt \ --egt /data/vitaled2/genomestudio/GSAv3Demo/Manifest_cluster_files/GSA-24v3-0_A1_ClusterFile.egt \ --bpm /data/vitaled2/genomestudio/GSAv3Demo/Manifest_cluster_files/GSA-24v3-0_A2.bpm \ --out /data/vitaled2/genomestudio/output

idat_paths.txt is just a text file with a different path to different sets of idats (must be from same chip-- i.e. same manifest and clusterfile). it looks like this:

/path/to/idats1/
/path/to/idats2/