inst/testScripts/complete/VUMC/61.AlleleCounts.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

#!/usr/bin/env Rscript

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#
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library("aroma.seq");


dataSet <- "AlbertsonD_2012-SCC,bwa,is";
organism <- "Homo_sapiens";

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# Setup
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# Annotation data
path <- file.path("annotationData", "organisms", organism);
filename <- "human_g1k_v37.fasta";
fa <- FastaReferenceFile(filename, path=path);
print(fa);

tags <- c("SNPs", "chr1-25");
ugp <- AromaUgpFile$byChipType("GenericHuman", tags=tags);
print(ugp);

# Data set
path <- file.path("bwaData", dataSet, organism);
bs <- BamDataSet$byPath(path);
print(bs);


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# Count allele for chromosome 22
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ac <- GatkAlleleCounting(bs, targetUgp=ugp, fa=fa);
print(ac);
dsC <- process(ac, verbose=verbose);
print(dsC);


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# HISTORY:
# 2012-10-31
# o Created.
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