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igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
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Request overhang softclip sequence view in igv reports #66

Closed julie-asimov closed 2 years ago

julie-asimov commented 2 years ago

In the desktop IGV viewer when softclip reads are selected it will show the overhands at the ends of the reference. This is extremely useful for whole plasmid sequencing. Is this something that can be mirrored for IGV reports?

jrobinso commented 2 years ago

igv.js side has been completed, transferring back to igv-reports

jrobinso commented 2 years ago

This is now supported with version 1.5.0

andyjslee commented 7 months ago

I used version 1.10.0 but don't see the softclip overhang. I ran the following code:

create_report test.bed \
  --genome hg38 \
  --flanking 10000 \
  --tracks test.bed test.bam \
  --output report.html

I see the softclip overhang on IGV but not in the HTML report generated by igv-reports. Is there a special option to enable display of softclip overhang?

jrobinso commented 7 months ago

You can right-click on the gear menu, but if you want to configure it to show by default you will have to use the track configuration option --track-config rather than or in addition to --tracks.

andyjslee commented 7 months ago

Thank you!

jrobinso commented 7 months ago

You're welcome. See the example. 

create_report test/data/variants/variants.vcf.gz \
--fasta https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa \
--ideogram test/data/hg38/cytoBandIdeo.txt \
--flanking 1000 \
--info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC \
--track-config test/data/variants/trackConfigs.json \
--output example_config.html