bwa-FQ score
Hi,
I use bwa and Annovar for mapping and SNP detection.
I want to know about Quality score in bwa out-put file.
I found that high Q score by bwa was correlated with the high SNP frequency (variant allele reads/mapped reads) by Clc bio software.
To define the SNPs finally, is it possible that I set the threshold value of Q score? How much score is appropriate?
In my analysis, I got totally 74 SNPs. The maximum and minimum score of Q are 228 and 3, respectively.
Thank you,
I use bwa and Annovar for mapping and SNP detection.
I want to know about Quality score in bwa out-put file.
I found that high Q score by bwa was correlated with the high SNP frequency (variant allele reads/mapped reads) by Clc bio software.
To define the SNPs finally, is it possible that I set the threshold value of Q score? How much score is appropriate?
In my analysis, I got totally 74 SNPs. The maximum and minimum score of Q are 228 and 3, respectively.
Thank you,
