Adding custom variants

[AGunnell77]

I am trying to use the edit variants function to add a list of SNPs I would like to view but they are not appearing on the track. The track name appears but I cannot see or search for any of my variants. I am uploading a local .bed file in which I have chromosome number in column 1(do I need chr or just number?) SNP position in columns 2 and 3 (can start and end position be the same?), rs ID in column 4 and probability in columns 5 and 6. Do the line endings need to be in a particular format eg CR LF?

[flekschas]

Your format sounds right assuming you provide hg19 coordinates (i.e., chr1, ...)

I've just tested it with the following format and it works:

chrom	start	end	variant	CredibleSet	Disease	pvalue	PosteriorProb	BestSNP	Coding	SpliceSite	Promoter	LocusID	Disease2
chr10	81147383	81147383	rs1250563	Huang2017-r114-1	IBD	19.92	0.2732	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81142475	81142475	rs1250573	Huang2017-r114-1	IBD	19.79	0.2334	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81146453	81146453	rs1250566	Huang2017-r114-1	IBD	19.73	0.1857	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81154692	81154692	rs199653515	Huang2017-r114-1	IBD	19.13	0.0467	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease

chrom	start	end	variant	CredibleSet	Disease	pvalue	PosteriorProb	BestSNP	Coding	SpliceSite	Promoter	LocusID	Disease2
chr10	81147383	81147383	rs1250563	Huang2017-r114-1	IBD	19.92	0.2732	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81142475	81142475	rs1250573	Huang2017-r114-1	IBD	19.79	0.2334	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81146453	81146453	rs1250566	Huang2017-r114-1	IBD	19.73	0.1857	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease
chr10	81154692	81154692	rs199653515	Huang2017-r114-1	IBD	19.13	0.0467	rs1250563	FALSE	FALSE	FALSE	57	Crohns_disease

[flekschas]

Did the format I posted help you visualize your custom variants?