Map hg19 whole exome data to exon number by gene

Question

[SunRise2019]

Hi,

I have a variants list obtained from whole exome sequencing:

WES table

I would like to map the variants to the exon number (exon1, exon2, exon3, etc.) for each gene. I am using hg19.

I tried biomart, but could not find the exon number for mapping.

Appreciate your help, thanks!

Answer 1

[swbarnes2]

Note that since genes have many transcripts, there will be no single way to number the exons in a gene.

Look for "exon rank in transcript".