CODEX2 Post-segmentation filters

[Layne Rogers]

Hello,

In the CODEX2 tutorial, there are recommended post-segmentation filters listed at the end of the tutorial:

"Post-segmentation pruning and filtering are recommended based on CNV length (filter1), length per exon (filter2), likelihood ratio (filter3), and number of exons (filter4)."

```

filter1 <- finalcall.CBS$length_kb<=200 filter2 <- finalcall.CBS$length_kb/(finalcall.CBS$ed_exon-finalcall.CBS$st_exon+1)<50 finalcall.CBS.filter <- finalcall.CBS[filter1 & filter2, ] filter3 <- finalcall.CBS.filter$lratio>40 filter4 <- (finalcall.CBS.filter$ed_exon-finalcall.CBS.filter$st_exon)>1 finalcall.CBS.filter=finalcall.CBS.filter[filter3|filter4,]

```

I am curious, how were these filters chosen/how were the thresholds determined? Is there any biological significance behind them?

I have been using CODEX2 to call CNVs and am unsure of whether or not I need to apply these filters and/or adjust the threshold values.

Thanks,

Layne