https://sourceforge.net/p/geneticthesaurus/wiki/Multiple%2520Samples/Recent changes to Multiple SamplesenTue, 28 Apr 2015 10:04:22 -0000https://sourceforge.net/p/geneticthesaurus/wiki/Multiple%2520Samples/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,5 +1,46 @@ ##Multiple Samples## -As of version 0.2.0, the software can annotate variants in matched samples. +As of version 0.2.0, the GeneticThesaurus software can annotate variants in matched samples. Applications may include search for somatic mutations in normal/tumor samples pairs in cancer genomics. +####Filtering variants#### + +Recall that the command to annotate variants in a simple sample is + + java -jar GeneticThesaurus.jar filter + --genome your.genome.fa + --bam alignment.bam + --vcf variants.vcf + --thesaurus thesaurus.tsv.gz + --output variants.thesaurus + +To process matched samples, extend this command with further arguments. Assuming that the samples are normal and tumor samples, the new command would look like this + + java -jar GeneticThesaurus.jar filter + --genome your.genome.fa + --bam tumor.bam + --label tumor + --vcf variants.tumor.vcf + --comparebam normal.bam + --comparelabel normal + --thesaurus thesaurus.tsv.gz + --output variants.thesaurus + +This contains three new arguments: *--label*, *--comparelabel* and *--comparebam*. + +The new *--label* argument provides a short descriptor for the primary sample for the analysis. In this example relevant for cancer genomics, the primary sample is the tumor sample. The alignment specified by *--bam* and the variants specified by *--vcf* are taken to correspond to this label. + +The other new arguments are *--comparelabel* and *--comparebam*. These specify a descriptor for the secondary sample and the corresponding alignment file. In this example, the secondary sample is the normal control matching to the tumor sample. + +Given this command with multiple alignment bam files, the software will start by scanning the tumor sample and annotating its variants in the usual way. Next, it will scan both the primary (tumor) and secondary (normal) samples to collect allelic frequency information on all the relevant genomic loci. + +The output of the matched samples command will consists, as usual, of several files with information about thesaurus annotations and allelic frequencies for the called variants. In the multi-sample analysis, the table with allelic frequencies will include columns pertaining to all the samples. + + + +####Calling changes across samples#### + +The filtering tool is meant to provide annotations for variants. It does not call mutations/differences across matched samples. However, the table with allelic frequencies output of the filtering tool can serve for this purpose. + +Package [RGeneticThesaurus](https://github.com/tkonopka/RGeneticThesaurus) provides handy functions for manipulating thesaurus annotations in the R environment. The vignette (in the inst/doc folder) shows a sample workflow for calling mutations in paired samples. + </pre> </div>TomaszTue, 28 Apr 2015 10:04:22 -0000https://sourceforge.net6eb6e3a628aee7a359d15637ce536d78dbb56e13https://sourceforge.net/p/geneticthesaurus/wiki/Multiple%2520Samples/<div class="markdown_content"><h2 id="multiple-samples">Multiple Samples</h2> <p>As of version 0.2.0, the software can annotate variants in matched samples.</p></div>TomaszTue, 28 Apr 2015 09:41:28 -0000https://sourceforge.net337e8f667ef18edbfc1f7c702526f8e1847d3438