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

Question

[samsara]

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

Answer 1

[Sean Davis]

• 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

Answer 2

[Chris Miller]

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

Answer 3

[galina.erikson]

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

[samsara]

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