Is It Necessary To Do Base Quality Score Recalibration Before Variants Detection In Gatk

Question

[Lds]

Hi,

As it mentioned in here, the reported base quality scores (the QUAL column in BAM file) before Base Quality Score Recalibration(BQSR) are neither very accurate nor informative, After recalibration, the quality scores in the QUAL field in each read in the output BAM are more accurate and then the reported quality score is closer to its actual probability of mismatching the reference genome. Is it necessary to do such step? How did the base quality affect the following variants detection?

Thanks in advance

Answer 1

[Zev.Kronenberg]

We do recalibration when there are multiple read groups. I believe it helps, but have no measures to back my claim. Try it both ways and see what you get. If you're trying to find disease genes eliminating any false positives really helps out.