Question: Intronic Variant Filtering
0
gravatar for cvu
2.7 years ago by
cvu150
India
cvu150 wrote:

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!!

variantcalling snp intron • 940 views
ADD COMMENTlink modified 2.7 years ago by Samuel Brady310 • written 2.7 years ago by cvu150
1
gravatar for Samuel Brady
2.7 years ago by
Samuel Brady310
Samuel Brady310 wrote:

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.

ADD COMMENTlink written 2.7 years ago by Samuel Brady310
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