list variants that map to a genomic location
The result of my awk script combines and formats all regions of a bed file containing 11 million bases, into targets less than a number of reads. For example, if there are 300 bases in chr1 less than 20 reads the output is:
chr1:1-300
Is there a tool besides igv that can identify known hg19 variants in this location? Maybe a database or file that can be used in a script. There is a similar feature in HGMD but it is more based on single positions. Thank you :).
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Its not clear, but Bedtools intersect might be what you are looking for. dbSNP snps can be used to overlap to regions of interest.
Thank you, I will try it out :)
See also answer to this question - Tabix might be what you are looking for.