Hi, I am using LoFreq in combination with another SNV caller. The other SNV caller lists quality scores as Q20, Q30, etc. My LoFreq output is giving a number string with the highest being 49314 in the QUAL column. How is this score calculated and how does it compare to a Phred score call like Q20?
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most variant callers produce rather arbitrary variant scores. LoFreq's
variant quality scores are"proper" error probabilities converted into a
Phred score. The error probabilities are computed using a poisson binomial
distribution, which takes all multiple quality scores (mapping quality,
alignment quality, base quality) into account. If you look up the
definition of Phred scores you will see that Q20 corresponds to an error
probability of 0.01, Q30 to 0.001 etc. 49314 is simply the lowest error
probability (highest quality) the system can represent.
Hi, I am using LoFreq in combination with another SNV caller. The other
SNV caller lists quality scores as Q20, Q30, etc. My LoFreq output is
giving a number string with the highest being 49314 in the QUAL column. How
is this score calculated and how does it compare to a Phred score call like
Q20?
Hi, I am using LoFreq in combination with another SNV caller. The other SNV caller lists quality scores as Q20, Q30, etc. My LoFreq output is giving a number string with the highest being 49314 in the QUAL column. How is this score calculated and how does it compare to a Phred score call like Q20?
Hi Catherine,
most variant callers produce rather arbitrary variant scores. LoFreq's
variant quality scores are"proper" error probabilities converted into a
Phred score. The error probabilities are computed using a poisson binomial
distribution, which takes all multiple quality scores (mapping quality,
alignment quality, base quality) into account. If you look up the
definition of Phred scores you will see that Q20 corresponds to an error
probability of 0.01, Q30 to 0.001 etc. 49314 is simply the lowest error
probability (highest quality) the system can represent.
Hope this helps,
Andreas
On Sat, 9 Jan 2021 at 03:01, Catherine Arnold kea027@users.sourceforge.net
wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | 0x7C68FBCC