Hi, I have a list of SNPs from a custom made microarray based on hg19/gb37. I need to extract all SNPs that are located in exons throughout whole genome. Is there a simple way to do this? Thanks in advance for your help
There are some programs that, having a gtf or gff file with your annotations, let you to extract regions of your genome. One of such programs is rgmatch
Thanks everyone for the answers. I don't think I have all the information required to generated gff (or GTF) file (https://genome.ucsc.edu/FAQ/FAQformat.html#format4) so I am not sure how to go about it. The SNP lists I've been dealing with have #rs (some with custom designations), chr, chr pos and genotyping data. In the past I used batch query in dbSNP but this is now defunct. If there is already workable solution (not involving programming) I would be grateful for a link. Apologies if this comment is duplicated as I haven't completely 'mastered' biostars system yet. Cheers Andy
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version 2.3.6
intersect gtf with bedtools.
input is missing :rs number, chrom/pos, ... ?
If you have rs number then may be you can use annotation based tools like wAnnovar, SNP nexus or VEP. These will exonic SNPs.