Has anyone tried using igv-reports on huge VCF files?
My VCF file is for 1 chromosome which has ~650 samples, with ~1M variants. I generated an html file using this code:
time create_report \
chrX.vcf.gz \
--fasta fasta.fa \
--title "IGV Variant ChrX" \
--output test_chrX.html \
> igv_report.out 2> igv_report.err
And generated an HTML file with 1.57 GB. I checked the html and saw that the variant info was embedded in the code but the html view only shows something like this
I'm thinking of splitting the vcf into chunks but the main reason for inspection via IGV is too see the vcf in whole and if splitting the chromosome during GATK genotypeGVCF might have missed some regions. I want to avoid standard IGV because I'm dealing with very huge VCF files, and this 1 chromosome I'm working on is an initial test.
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1 answer
A 1.6 GB HTML file is likely too large for most modern web browsers to handle efficiently. The developers of igv-reports indicate that a ~100 MB report is already near the upper limit for browser-based inspection.
Ref: https://academic.oup.com/bioinformatics/article/42/4/btag125/8513491#561650257
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