I'm just getting started, so hopefully this isn't a silly post.
Mosaik and some other aligners are able to use IUPAC codes in their alignment process.
I was wondering if there are any publicly available whole genome reference sequences available that contain the IUPAC codes for known SNPs. If not, I was curious if there are any applications that can apply these codes via data from dbSNP, etc., or if I would be better off coding something to handle this.
Thanks!
Mosaik and some other aligners are able to use IUPAC codes in their alignment process.
I was wondering if there are any publicly available whole genome reference sequences available that contain the IUPAC codes for known SNPs. If not, I was curious if there are any applications that can apply these codes via data from dbSNP, etc., or if I would be better off coding something to handle this.
Thanks!
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