inst/testScripts/complete/VUMC/21.TotalCNs.R

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

#!/usr/bin/env Rscript

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library("aroma.seq");

dataSet <- "AlbertsonD_2012-SCC";
organism <- "Homo_sapiens";

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

# Data set
path <- file.path("fastqData", dataSet, organism);
ds <- IlluminaFastqDataSet$byPath(path);
print(ds);

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# Build BWA index set
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is <- buildBwaIndexSet(fa, verbose=-10);
print(is);


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# Single-end alignment
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# Process at most two FASTQ files
ds <- extract(ds, 1:min(3, length(ds)));

# In addition to SAM read group data inferred from the Illumina FASTQ
# files, manual set the library information for the whole data set.
setSamReadGroup(ds, SamReadGroup(LB="MPS-034"));

# BWA with BWA 'aln' options '-n 2' and '-q 40'.
alg <- BwaAlignment(ds, indexSet=is, n=2, q=40);
print(alg);

bs <- process(alg, verbose=-20);
print(bs);


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# Remove duplicated reads using Picard
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dr <- PicardDuplicateRemoval(bs);
print(dr);

bsU <- process(dr, verbose=-20);
print(bsU);



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# HISTORY:
# 2012-10-02
# o Created.
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