Intronic Variant Filtering

Question

[cvu]

Hello all,

I want to filter variants based on their genomic location.

For example RSID rs10863805, this variant is Intronic variant and it is 18 nucleotides away from exon and I want to keep all intronic variants which falls in before or after 100 nucleotides of exon region.

5'-------INTRON--------100bp-------EXON-------100bp---------INTRON------------3'
                            ^----------------^

I want all variants which are in the highlighted region from the figure above.

Thanks in advance!

Answer 1

[Samuel Brady]

You can find the locations of exons (for hg19) from UCSC here: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz

Columns 10 and 11 show you the start and end sites, respectively, of exons. Make sure the genome build you are using matches the build you download from UCSC.