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Old 09-07-2015, 08:50 AM   #2
Location: Cambridge, MA

Join Date: Apr 2011
Posts: 18

If you are looking to test whether mutations identified by WES are present in your single cells, you should be able to use standard SNP calling tools, although you might do better by doing a pileup at those locations and setting a threshold. You didn't specify how you are doing the whole genome amplification, but with any method you should expect a fairly high allele dropout rate--cases in which the cell contains a heterozygous mutation that isn't detected. You can test for this by checking what fraction of known heterozygous SNPs are detected by your algorithm.

If you want to identify new mutations that weren't in your WES data, this becomes much more difficult. The main challenge is that there will be thousands of false positives due to errors by the polymerase during amplification.

For metrics like alignment rate, we recently had a review paper that compares the performance of WGA different kits:
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