Implemented a minimally invasive approach for processing Tumor-only HTS (WGS) data with the latest ASCAT version.
Highlights are as follows:
ascat.prepareHTS will now run in tumor-only mode (and print this to the user) when no normal bam is provided.
alleleCount is run on tumor only (duh) and the same counts are internally assigned to the normal, but not used or written to disk
ascat.getBAFsAndLogR now has a tumor_only_mode=F default argument which gets set within ascat.prepareHTS
Tumour LogR is calculated as log2(Tumour_Counts / mean(Tumour_Counts))
Germline genotypes are inferred using ascat.predictGermlineGenotypes which has a new preset HTS_WGS_1000G which was tuned on in-house WGS data using the 1000G hg38 panel of loci provided with ASCAT.
Thanks for providing the tumor-only code for HTS. Will this also work for targeted seq? If not, is there a plan to integrate tumor-only mode for targeted seq?
Implemented a minimally invasive approach for processing Tumor-only HTS (WGS) data with the latest ASCAT version. Highlights are as follows:
ascat.prepareHTS
will now run in tumor-only mode (andprint
this to the user) when no normal bam is provided.alleleCount
is run on tumor only (duh) and the same counts are internally assigned to the normal, but not used or written to diskascat.getBAFsAndLogR
now has atumor_only_mode=F
default argument which gets set withinascat.prepareHTS
log2(Tumour_Counts / mean(Tumour_Counts))
ascat.predictGermlineGenotypes
which has a new presetHTS_WGS_1000G
which was tuned on in-house WGS data using the 1000G hg38 panel of loci provided with ASCAT.