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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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igv/sample.xml file writes wrong reference genome (37 instead of 38) #43

Open OlenaMaiakovska opened 1 year ago

OlenaMaiakovska commented 1 year ago

Hi all, I run into issue of xml file generation with wrong reference genome. When I submit the run using command:

input_path=/input_dir/ refdata_path=$PWD/clinsv/refdata-b38 project_folder=$PWD/449_WT docker run -v $refdata_path:/app/ref-data -v $project_folder:/app/project_folder -v $input_path:/app/input --entrypoint "perl" mrbradley2/clinsv:v1.0 /app/clinsv/bin/clinsv -r all -p /app/project_folder/ -i "/app/input/*.bam" -ref /app/ref-data/refdata-b38

it successfully completes the process and generates all expected output files. However, igv folder has the file with following resources information: <?xml version="1.0" encoding="UTF-8" standalone="no"?>

Obviously, when I load it into igv it can not allocate wrong reference. Is there problem from my side (since I used ref 37 before while attempting to run test file but later deleted all 37 ref files) or something is code automation that results in ref 37 by default? thank you very much for troublshooting in advance! Best, Olena
drmjc commented 1 year ago

Thanks Olena. In the IGV XML file, what reference genome is selected? If it's not <Session genome="hg38" version="8"> or similar, can you edit this and see if it solves the problem? Can you also let me know the URL's for some of the annotation tracks, to see if they're selecting hg38 ones or not?

Also the nci.space server is currently down which will affect the downloading of annotation tracks (see #44).

drmjc commented 1 year ago

I've been looking at this, and indeed the IGV session XML file is not correct for hg38. working on a solution.