tlesluyes
commented
1 year ago Hi @jffpviana,
That's right: ascat.prepareTargetedSeq just requires the allele files, not the loci ones. At the end of this function, cleaned allele and loci files will be created, they need to be fed into ascat.prepareHTS.
Please note that we have made a few changes in the code in such a way that ASCAT will ask for a reference genome, either hg19 or hg38. We'll allow people processing non-human HTS data in the future but it will probably take a few months to get there. In the meantime, I suggest you set all samples to 'female' and use 'hg38', but don't consider copy-number status for chrX.
Cheers,
Tom.
Hi, I want to use ASCAT on targeted sequencing data from cats and dogs. I'm trying to understand what is the format needed of the allele file for ascat.prepareTargetedSeq(). The example given in the WES reference file only has the positions and the alleles and a separate loci file would be needed with chromosome information. But the loci file doesn't seem to be an argument of the ascat.prepareTargetedSeq function. Thanks in advance!