The same directory as the BAM file itself. The BAM files need to be indexed with the samtools index command and located in Triple BAM method that land in genes with high sequence similarity. RADIA uses SnpEff to annotate passing variants and to filter out calls from the SnpEff (optional, tested on version 3.3 and 4.3) RADIA uses BLAT to check the mapping of reads for all Triple BAM calls. RADIA uses the pysam API during the filtering process.
#RADIA ENTERPRISES INSTALL#
You must install samtools prior to running RADIA. RADIA uses samtools to examine pileups of reads across each sample in parallel. Samtools (tested on version 0.1.18 and 0.1.19) The RADIA code is written and compiled in python. Traditional methods that only interrogate the DNA. RNA RescueĬalls are those that had very little DNA support, hence not called by the DOM, but strong RNA Confirmation calls are those that are made byīoth the DOM and the TBM due to the strong read support in both the DNA and RNA. The mutations from the TBM are further categorized into 2 sub-groups: RNAĬonfirmation and RNA Rescue calls. While the Triple BAM Method (TBM) uses all three datasets from the same patient to detect The DNA Only Method (DOM) uses just the tumor/normal pairs of DNA (ignoring the RNA), Tumor RNA to identify potential RNA editing events. Tumor DNA and tumor RNA to augment the somatic mutation calls. For the tumor DNA, RADIA outputs any differences compared to the referenceĪnd the normal DNA which could be potential Somatic mutations. Outputs any differences compared to the reference which could be potential Germline If no RNA is availableįrom the tumor, then it is run on the normal/tumor DNA pairs. RADIA is typically run on 3 BAMįiles consisting of the Normal DNA, Tumor DNA and Tumor RNA. RADIA identifies RNA and DNA variants in BAM files.
0 kommentar(er)
