Question: mpileup result uncertanties, what does "<*>" mean?!?!?
gravatar for beckybedford96
4 weeks ago by
beckybedford960 wrote:

I am trying to userstand the results from the mpile up tool but I am unsure what the "<*>" is in the alt column is? It also appears in conjunction in another base. What does it mean?!? ='(

ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson24k • written 4 weeks ago by beckybedford960
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:


The * represents a deletion in the reference genome.

From the VCF Specification:

ALT - alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or an angle-bracketed ID String (“<id>”) or a breakend replacement string as described in the section on breakends. The * allele is reserved to indicate that the allele is missing due to a upstream deletion. If there are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas, or angle-brackets are permitted in the ID String itself)

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 15 hours ago • written 4 weeks ago by Jennifer Hillman Jackson24k
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