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Old 04-19-2012, 09:58 AM   #1
half_programmer
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Default Questions about snp annotation format in old vcf

Hi, all,

In old vcf format, for SNP annotation, the substituion or alternative alleles could be 'A T C G Y S M R K W' etc. Does anyone know some clues about these 'Y S M R K W' etc?
Thank you.

Kindly Regards
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Old 04-19-2012, 10:04 AM   #2
swbarnes2
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Those other letters are codes for ambigous letter. In the context of a SNP, it means a mixed SNP, a heterozygote, if you are dealing with a diploid organism

See here. (rememebring what all the letters means helps remember which letter stands for which pair)

http://en.wikipedia.org/wiki/Nucleic_acid_notation
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Old 04-19-2012, 10:53 AM   #3
half_programmer
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Quote:
Originally Posted by swbarnes2 View Post
Those other letters are codes for ambigous letter. In the context of a SNP, it means a mixed SNP, a heterozygote, if you are dealing with a diploid organism

See here. (rememebring what all the letters means helps remember which letter stands for which pair)

http://en.wikipedia.org/wiki/Nucleic_acid_notation
Thank you, it really answered my question.
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