What Is The Most Commonly Used File Format For Storing Copy Number Variation Data?

What is the most commonly used file format for storing Copy Number Variation data?

cnv

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updated 12.7 years ago by Chris Miller

• written 12.7 years ago by samsara

3 answers

The so-called "segment" format is one such format:

http://www.broadinstitute.org/igv/SEG

http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/linked_files/example.seg

The VCF format can also describe CNV regions:

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

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written 12.7 years ago by Sean Davis

DNAcopy output is very common - 6col (sample, chr, start, stop, num.probes, seg.mean)

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written 12.7 years ago by Chris Miller

CNVnator: http://www.ncbi.nlm.nih.gov/pubmed/21324876 Download: http://sv.gersteinlab.org/

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written 12.7 years ago by galina.erikson

I am not in need of any tool to discover CNVs.

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written 12.7 years ago by samsara

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