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dmcblab / InfoGenomeR

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Exome data #6

Closed jgarces02 closed 1 year ago

jgarces02 commented 1 year ago

Hi, is it possible to apply this (interesting) package to exome sequencing data? (I think all required inputs could be also available from WES...).

Thanks

dmcblab commented 1 year ago

In some way, the breakpoint graph construction step might be possible for WES. However, It will be painful to fine-tune CNV/SV parameters. In addition, some tools used in InfoGenomeR may not work for WES. I have not tried yet. The allele-specific and haplotype graph step will not be possible for WES as well.

I recommend other exome-specific tools that can detect CNVs and SVs in WES.

Thanks!