Intronic Variant Filtering
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Entering edit mode
4.4 years ago
cvu ▴ 180

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 bold region from above figure.

Thanks in advance!!

snp variantcalling intron • 1.4k views
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Entering edit mode
4.4 years ago
Samuel Brady ▴ 320

You can find the locations of exons (for hg19) from UCSC here:

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.

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