in DEFAULT FOR TCGA, are all SNP called without CpG context called as well?

[Lorena Pantano]

Hi,

thanks to maintaining and developing this tool! is amazing!

I am trying some rrbs data, and we are interesting to get all SNPs, not only the ones inside a CpG context. With the default option is this the case?

I just want to make sure, I am not ignoring other kinds of SNPs with this option.

thanks a lot again for your time!

[ping]

Hi Lorena,

Thanks for your interests! All potential SNPs are called at snp.vcf file by default. A lot of SNP are in CpG Context, but some are not.

yaping

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Yaping Liu, Ph.D.

Postdoctoral Associate

Manolis Kellis Lab

Computer Science and Artificial Intelligence Lab (CSAIL)
Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

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[Lorena Pantano]

thanks a lot for your quick reply!