Hi there,
I have succeed to do the variant calling through Samtools and bcftools, but
there are still some questions that confusing me.
1.What is the statistical method used in Samtools ? I've checked many
documentions but only found the mathematical formula for likelihood in
2011,Heng L. Is the statistical method free Bayesian or others? Are there any
links to explain the statistical method?
2.As the discription in Samtools manual page, Samtools mpileup just
"computes the likelihood of data given each possible genotype", buf for
bcftools, "bcftools applies the prior and does the actual calling". When I
explored the difference of results between Samtools mpileup and bcftools
call(I've translated these BCF format file to VCF format file through
bcftools), the value of QUAL and the genotype differ in two files. Here is the
screeshot of mpileup results
and the call results ,the QUAL values changed from 9.52546 in mpileup to
11.4963 in call, the genotype(GT) altered from 1/1 to 0/1 as well. I used the
samtools and bcftools both in version 1.2. Are there anyone that understand the
calculation and convertion done by bcftools call? Why does the mpileup and call
give different QUAL and genotype?
Best wishes,
Yang
--------------
Yang Xiaoxue,
Master student,
Southern Medical Unversity,
email: [email protected]------------------------------------------------------------------------------
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