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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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default min.mapq #29

Closed josianne-bioinf closed 4 years ago

josianne-bioinf commented 4 years ago

Hi,

What is the default min MQ value is when running getBamCounts? I've tried setting it to 20 and to 1, but the results are not the same as when I run it without specifying the min.mapq argument.

Thank you, Josianne