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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Do I need to set "--target" option for exome data? #56

Closed jeffchen2000 closed 1 year ago

jeffchen2000 commented 1 year ago

Dear Dariober I have exome data, (say from SureSelect probe), should I set "--target" option like this: "--target SureSelect_probe.bed"

or if you can provide a recommended/example of full command for exome data will be very help! thanks Jeff C

dariober commented 1 year ago

Hi- Yes, --target SureSelect_probe.bed is what I would do. E.g.:

cnv_facets.R --target SureSelect_probe.bed -t <tumour.bam> -n <normal.bam> -vcf <snps.vcf.gz> -o <output_prefix>

as for other use cases, you may need to tweak some analysis parameters to improve results (see the README and the documentation of the FACETS package).