known indel database for detecting somatic lesions in tumor

csoong · 01-05-2011, 09:04 AM

Hi,

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,
CSoong

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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01-05-2011, 09:04 AM	#1
csoong Member Location: Connecticut Join Date: Jun 2009 Posts: 74	known indel database for detecting somatic lesions in tumor Hi, 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, CSoong 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.