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Old 01-05-2011, 09:04 AM   #1
Location: Connecticut

Join Date: Jun 2009
Posts: 74
Default known indel database for detecting somatic lesions in tumor


This may have been discussed before but I couldn't find the right info.
I am trying to identify somatic lesions in tumor DNA.
For point mutations, I use ucsc snp131 single base entries to screen out common polymorphisms.
For indels, however, ucsc snp131 entries are not positioned to left most base location. As a result, my dindel/samtools output cannot be directly compared with the ucsc snp131 indel entries.

Does anyone know where such left-most positioned indel database can be found?

Thanks in advance,

PS: I also have germline sequencing data coming along, but for now I was hoping to do some prelim analysis with know indel polymorphism in the population.
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