igvteam/igv.js

VariantTrack header.INFO undefined

Closed this issue · 1 comments

Hello again,

This time I get the following error for this line:
TypeError: Cannot convert undefined or null to object

I am using a pretty blank VCF file:

##fileformat=VCFv4.2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr6	63498622	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779765' target='_blank'>rs1779765</a>	T	A	.	.	.
chr6	63498633	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779766' target='_blank'>rs1779766</a>	G	A	.	.	.
chr6	63498639	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779767' target='_blank'>rs1779767</a>	G	A	.	.	.

I performed some tests:

  1. Replaced the dots in the INFO column through dummy values, did not change anything
  2. Added an additional row ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency" at the beginning - this solved it. SNPs appeared grey if only a dot was present in the INFO column.

How I hope this could work:

  • Additional header fields should be optional
  • If no header fields are present, the SNPs should be visualized in the standard blue, so that they are more easily visible

Thank you for maintaining this great package!

Thank you very much!