dnanexus_ED_cnv_analysis_v1.3.1

Performs CNV calling using ExomeDepth.

Exome depth is run in two stages. Firstly, read counts are calculated, before CNVs are called using the read counts. Read counts are calculated over the entire genome whereas the CNV calling can be performed using a subpanel.

What does the app do?

This app runs the CNV calling stage.

How the app works?

A Docker image containing Exome depth is downloaded from 001 - The image is taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.1.0 The app takes in a readcount file generated by https://github.com/moka-guys/dnanexus\_ED\_readcount_analysis, the docker image will pick the most appropriate reference samples and run exomedepth for a given sample.

For further details on the usage of the docker image please refer to https://github.com/moka-guys/seglh-cnv/tree/main/exomedepth

Input

• DNAnexus project name where the BAM and the indexes are stored (BAMs/BAIs MUST be present in the /output folder)
• Readcount file generated using https://github.com/moka-guys/dnanexus\_ED\_readcount_analysis
• List of comma seperated pan numbers (Pan4127,Pan4129,Pan4130,Pan4049)
• Test specific BED file
• reference genome file (hs37d5.fa.gz) Note: Transitional probability is set to 0.01, the default value is 0.001 (too many false positives during testing). See CLI command below for an example of inputs.

Output

• output.pdf - Exomedepth CNV report with all QC information
• output.tex - Intermediate file used to create PDF
• tables-1.pdf, tables-2.pdf etc - Plots for inclusion in the generated reports
• output.bed - CNVs in BED format (whole panel)
• output.RData
• output.vcf

Running from the CLI:

The app can be run from the dx CLI. The example below shows the code used to run test samples through this app:

dx run project-G0pKxX80pgqFk9Vy8p6vQbKv:applet-G7B5Zxj0pgq9Q8JfP0jpY3y4 -iproject_name=003_220103_exomeDepth_calling_test -ireadcount_file=project-G6jb1k807Xjj1J984K6kfP13:file-G6kg5q80gvvz37qZ4ZPbvZ8Q -ibamfile_pannumbers=Pan4127,Pan4129,Pan4130,Pan4049 -isubpanel_bed=project-ByfFPz00jy1fk6PjpZ95F27J:file-G6kZpqQ0jy1q1Zk94G3qbVyV -ireference_genome=project-ByfFPz00jy1fk6PjpZ95F27J:file-B6ZY7VG2J35Vfvpkj8y0KZ01

Debugging

For debugging issues with the docker image it can be helpful to ssh into a 'held for debugging' job in DNA nexus and run the docker image in interactive mode:

docker run -v /home/dnanexus:/home/dnanexus/ --rm -it --entrypoint /bin/bash seglh/exomedepth:87fa493