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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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LINX visualization for select regions #395

Closed lichennan123 closed 1 year ago

lichennan123 commented 1 year ago

Hi LINX developers,

I would like to view a particular SV chain within a cluster that crosses three genomic locations. Here is the script that I used:

java -cp /data/lic27/tools/linx_v1.22.jar com.hartwig.hmftools.linx.visualiser.SvVisualiser \
    -sample SAMPLE \
    -ensembl_data_dir /data/lic27/tools/linx/ensembl_data/ \
    -ref_genome_version 38 \
    -plot_out /data/lic27/linx/linx_visual/plot \
    -data_out /data/lic27/linx/linx_visual/data \
    -vis_file_dir /data/lic27/linx/linx \
    -circos /data/lic27/tools/circos/circos-0.69-9/bin/circos \
    -clusterId 317 \
    -chromosome chr10,chr12,chr17 \
    -specific_regions chr10:9300000:9370000;chr12:45798000:45803000;chr17:3000000:8000000

I realized the script above was run without the last portion (chr12/chr17 regions) due to the semicolon which is specified in the manual - the argument 'specific_regions'. I was able to view each of the three locations separately. Just wondered if there are any suggestions for viewing the entire chain (rather than the whole cluster) as a whole. Thank you for any thoughts and creating such a great tool!

Sincerely, Chennan

lichennan123 commented 1 year ago

Any response? It is okay if this is not an option at all and I can try figuring out some other ways. Thanks!

charlesshale commented 1 year ago

This is possible in LInx 1.23.6 which will be released later this week.

charlesshale commented 1 year ago

See: https://github.com/hartwigmedical/hmftools/releases/tag/linx-v1.23.6