Hi!
I guess a lot of you have read this one:
Nat Methods. 2013 February ; 10(2): 128–132. doi:10.1038/nmeth.2330
I have some question about the filtering they use:
1. They exclude SNPs which are found in dbSNP, except SNPs of molecular type “cDNA”. How is this done?
2. They also discarded mismatches in the first six bases of each read to avoid artificial mismatches derived from random-hexamer priming. Can this be done AFTER alignment? i.e in a called vcf file?
Thanks a lot!
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