From the MAQ paper Li et al (2008) it is assumed that,
Let P(<b,b’>) = r, then P(<b,b>) = P(<b’,b’>) = (1 - r)/2
–r is the probability of observing a heterozygote
–if there is a known SNP in the position (dbSNP or OMIM), r = 0.2.
Otherwise, r=0.001. One can also use site specific allele frequency"
From the paper Li et al (2009) it was mentioned that
"Other information that can be used in setting priors: – Use dbSNP prior
– Use different polymorphism rate for different genomic region
– Consider different Ti/Tv rate for exonic regions"
Which of these prior probabilities are used in samtools by default, for
example for a non-human genome?
Does the prior set in samtools differ from the prior set in GATK?
Get latest updates about Open Source Projects, Conferences and News.