Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.

Question

[sktbanerjee1]

I am trying to call variants from whole exome paired end sequences aligned to HG38p7 using the Freebayes variant caller. As it is a general recommendation to perform BQSR before any type of variant calling, I was wondering is it necessary to perform the BQSR before calling variants with freebayes?

Answer 1

[finswimmer]

Hello,

the authors of freebayes itself are saying, that neither BQSR nor VQSR is neccessary.

fin swimmer

[xuzhougeng]

Could you tell me where can I find the original that "the authors of freebayes itself are saying, that neither BQSR nor VQSR is neccessary." I want to find out why BQSR is unnecessary

[finswimmer]

Hello, just follow the link in my post and you will find it. A copy and paste from the website:

FreeBayes incorporates a number of features in order to reduce the complexity of variant detection for researchers and developers:

Indel realignment is accomplished internally using a read-independent method, and issues resulting from discordant alignments are dramatically reducedy through the direct detection of haplotypes.

The need for base quality recalibration is avoided through the direct detection of haplotypes. Sequencing platform errors tend to cluster (e.g. at the ends of reads), and generate unique, non-repeating haplotypes at a given locus.

Variant quality recalibration is avoided by incorporating a number of metrics, such as read placement bias and allele balance, directly into the Bayesian model. (Our upcoming publication will discuss this in more detail.)