Question: Map quality difference in Varscan somatic
gravatar for andxiwang
5.2 years ago by
andxiwang0 wrote:

I am a little confused about "Map quality difference " of somatic SNV calling package in varscan 2. 

As described in Table 1.  (Koboldt D C, Zhang Q, Larson D E, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing[J]. Genome research, 2012, 22(3): 568-576.)

"Difference in average mapping quality between reference and variant reads", is it means that | average_mapping_quality_reference_reads - average_mapping_quality_of_variant_reads) <= 30 ?


I am thinking about filtering low mapping quality variants in my genomic data, is it suitable if we apply Wilcoxon rank sum test to calculate significance between variant reads and mapping quality thresholds (eg. 20)

Thank you!

snv next-gen varscan • 1.5k views
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