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Applying BQSR before running GATK's HaplotypeCaller on whole-genome sequencing data

Hi all,

I'm trying to do variant calling on sequencing data (Illumina Hiseq) resulted from whole-genome sequencing of a given population via GATK. The sequencing technology and bioinformatic packages upgraded regularly; also, some regions in the human genome show high sequence divergence from the reference genome, specifically, it can be true for genome sequencing of a given population as in my case. That's why performing base quality score recalibration (BQSR) before running the HaplotypeCaller on my BAM files is so unclear and confusing to me. In your professional view, running BQSR on my samples can be beneficial or deleterious? Could you please share me your helpful suggestions and help me to make a right decision?

Thank you in advance

variant calling haplotypecaller
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updated by finswimmer finswimmer • written by seta seta

1 answer

Hello seta,

BQSR changes the quality values for each base within the reads which initially was set by the sequencing machine. The goal (or the hope) behind this is, that the new values are nearer to the truth. This changed quality values influences the mappibilty and alignment of the reads and may have influence to the variant calling.

That's the theory. My opinion is, as long as your overall base quality is good, there is no need to run BQSR. The benifit will be very low but the process itself is time consuming. In low diversity genomes I can imagine that the benift will be much higher.

Also have a look at this thread some time ago about this topic:

fin swimmer

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written by finswimmer finswimmer

Hi Fin swimmer, Thank you. As the overall base quality is good, especially trimming was also done before and data came from a given population with high diversity, I decided not to do BQSR based on your explanation.

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written by seta seta

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