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bands and cram tracks are not loading on igvjs 3.0.5 they worked fine on 2.15.9 #123

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barslmn opened this issue Dec 28, 2024 · 0 comments

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@barslmn
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barslmn commented Dec 28, 2024

Hi,
I created the reports with the following command:

create_report /mnt/dragen/baris/epi25/dragen/exomiser_results/E05-60/E05-60.hard-filtered.withPhenotype.vcf.variants.tsv 
    --fasta /staging/references/hg38-alt_masked.cnv.graph.hla.rna-9-r3/hg38-custom-reference-genome-1.1.0/hg38.fa 
    --ideogram /staging/references/hg38-alt_masked.cnv.graph.hla.rna-9-r3/hg38-custom-reference-genome-1.1.0/cytoBandIdeo.txt 
    --sequence 15 --begin 16 --end 17 --flanking 1000 
    --info-columns RANK ID GENE_SYMBOL ENTREZ_GENE_ID MOI P-VALUE EXOMISER_GENE_COMBINED_SCORE EXOMISER_GENE_PHENO_SCORE EXOMISER_GENE_VARIANT_SCORE EXOMISER_VARIANT_SCORE CONTRIBUTING_VARIANT WHITELIST_VARIANT VCF_ID RS_ID CONTIG START END REF ALT CHANGE_LENGTH QUAL FILTER GENOTYPE FUNCTIONAL_CLASS HGVS EXOMISER_ACMG_CLASSIFICATION EXOMISER_ACMG_EVIDENCE EXOMISER_ACMG_DISEASE_ID EXOMISER_ACMG_DISEASE_NAME CLINVAR_ALLELE_ID CLINVAR_PRIMARY_INTERPRETATION CLINVAR_STAR_RATING GENE_CONSTRAINT_LOEUF GENE_CONSTRAINT_LOEUF_LOWER GENE_CONSTRAINT_LOEUF_UPPER MAX_FREQ_SOURCE MAX_FREQ ALL_FREQ MAX_PATH_SOURCE MAX_PATH ALL_PATH 
    --tracks /mnt/dragen/baris/epi25/dragen/hg38_joint_genotyping/samples/filtered/E05-60.hard-filtered.withPhenotype.vcf.gz /mnt/dragen/baris/epi25/dragen/hg38_results/E05-60/E05-60.cram /staging/references/hg38-alt_masked.cnv.graph.hla.rna-9-r3/ncbiRefSeq.txt.gz 
    --output igv_reports/E05-60.withPhenotype.igv_mqc.html

Back in an older version it worked. I installed the newer version and chromosome bands and cram tracks were not being displayed.
I changed the igvjs version in the script tag to 2.15.9 and the tracks were visible again.
There were no errors on chrome console.

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