VIGNETTES: SNP6 Copy Number Component Workflow

Date:

2008-06-18

Contents

• apt-probeset-genotype: Generating signal estimates and genotyping calls.
• apt-copynumber-reference: Loading CN5 data into a reference file.
• apt-copynumber-log2ratio: Generating log2 ratios and allelic differences.
• apt-copynumber-analysis: Generating CN5 analysis data.
• FAQ - Frequently Asked Questions.

apt-probeset-genotype: Generating signal estimates and genotyping calls.

APT supports output of signal estimates and genotype calls on a per SNP or per CN probeset basis. The default analysis recommends quantile normalization (quant-norm) across all chips.

For SNPs, in SNP 6 chips signal estimates will be provided for the A-allele and the B-allele. CN probesets will have one signal estimate value.

You can use "apt-probeset-genotype --help" for more information on command line arguments and any of the following to get more information about the various analysis stream components:

    apt-probeset-genotype --explain quant-norm
    apt-probeset-genotype --explain pm-only
    apt-probeset-genotype --explain plier

This is an example of how to a do apt-probeset-genotype run for CN5 using APT:

    apt-probeset-genotype \
	--feat-effects false \
	--write-sketch false \
	--write-models false \
	--set-analysis-name Test \
	--a5-use-global true \
	--a5-sketch true \
	--a5-sketch-use-global true \
	--a5-feature-effects true \
	--a5-feature-effects-use-global true \
	--a5-write-models true \
	--a5-write-models-use-global true \
	--a5-global-file output_directory_name/CNReference.a5.ref \
	--a5-calls true \
	--a5-calls-use-global false \
	--a5-confs true \
	--a5-confs-use-global false \
	--a5-residuals false \
	--a5-residuals-use-global false \
	--a5-summaries true \
	--all-types true \
	--summaries true \
	--netaffx-snp-annotation-file lib_directory_name/GenomeWideSNP_6.na25.annot.csv \
	--netaffx-cn-annotation-file lib_directory_name/GenomeWideSNP_6.cn.na25.annot.csv \
	--cdf-file lib_directory_name/GenomeWideSNP_6.cdf \
	--qmethod-spec plier.optmethod=1.FixFeatureEffect=true \
	--a adapter-type-norm,quant-norm,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.HARD=3.SB=0.45.KX=1.KH=1.5.KXX=0.5.KAH=-0.6.KHB=-0.6.transform=MVA.AAM=2.0.BBM=-2.0.AAV=0.06.BBV=0.06.ABV=0.06.copyqc=0.wobble=0.05.MS=0.05 \
	--set-gender-method cn-probe-chrXY-ratio \
	--chrX-probes lib_directory_name/GenomeWideSNP_6.chrXprobes \
	--chrY-probes lib_directory_name/GenomeWideSNP_6.chrYprobes \
	--special-snps lib_directory_name/GenomeWideSNP_6.specialsnps \
	--out-dir output_directory_name \
        celfile_directory/*.CEL

Note that the use of wild cards (*.CEL) is dependent on the shell from which the command is run. For example, the default shell on Windows does not support wild card expansions, so you will probably want to use the "--cel-files" option instead.

apt-copynumber-reference: Loading CN5 data into reference file.

apt-copynumber-reference will produce a CN5 reference file that can be used later to run single samples.

You can use "apt-copynumber-reference --help" for more information on command line arguments.

This is an example of how to a do CN reference run using APT:

    apt-copynumber-reference \
	--set-analysis-name Test \
	--hdf5-output true \
	--text-output false \	
	--log2-input false \
	--netaffx-snp-annotation-file lib_directory_name/GenomeWideSNP_6.na25.annot.csv \
	--netaffx-cn-annotation-file lib_directory_name/GenomeWideSNP_6.cn.na25.annot.csv \
	--reference-file input_directory_name/CNReference.a5.ref \
	--x input_directory_name/Test.plier.summary.a5 \
	--genotype-calls-file input_directory_name/Test.calls.a5 \
	--genotype-confidences-file input_directory_name/Test.confidences.a5 \
	--genotype-report-file input_directory_name/Test.report.txt \
	--out-dir output_directory_name

apt-copynumber-log2ratio: Generating log2 ratios and allelic differences.

You can use "apt-copynumber-log2ratio --help" for more information on command line arguments.

This is an example of how to a do CN log2ratio run using APT:

    apt-copynumber-log2ratio \
	--set-analysis-name Test \
	--log2-input false \
	--hdf5-output true \
	--text-output false \
	--cnchp-output false \
	--call-copynumber false \
	--netaffx-snp-annotation-file lib_directory_name/GenomeWideSNP_6.na25.annot.csv \
	--netaffx-cn-annotation-file lib_directory_name/GenomeWideSNP_6.cn.na25.annot.csv \
	--reference-file input_directory_name/CNReference.a5.ref \
	--x input_directory_name/Test.plier.summary.a5 \
	--genotype-calls-file input_directory_name/Test.calls.a5 \
	--genotype-confidences-file input_directory_name/Test.confidences.a5 \
	--genotype-report-file input_directory_name/Test.report.txt \
	--out-dir output_directory_name

apt-copynumber-analysis: Generating CN5 analysis data.

You can use "apt-copynumber-analysis --help" for more information on command line arguments and any of the following to get more information about the various analysis stream components:

    apt-copynumber-analysis --explain cn-state
    apt-copynumber-analysis --explain loh
    apt-copynumber-analysis --explain gaussian-smooth

This is an example of how to a do CN analysis run using APT:

    apt-copynumber-analysis \
        --array-name GenomeWideSNP_6 \
	--text-output true \
	--set-analysis-name Test \
	--log2ratio-file input_directory/Test.NA06985_GW6_C.cel.a5 \
	--out-dir output_directory_name

Frequently Asked Questions

Q. Are there similar recommendations for snp array 5?

A. No. This workflow may not produce meaningful results with the SNP 5.0 array. If you are interested in a copy number analysis software solution for SNP 5.0 arrays, please check out the various GeneChip Compatible partner solutions, http://www.affymetrix.com/products/software/compatible/index.affx .

Affymetrix Power Tools (APT) Release apt-1.10.1

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