Copy number aberrations / Add cytogenetic bands

Description

Adds the cytogenetic band information using chromosome names and start/end base pair positions. If this position information is not present in your data set, please first add it using the tool Fetch probe positions from GEO / CanGEM.

Parameters

• Human genome build to use (GRCh37/hg19, NCBI36/hg18, NCBI35/hg17, NCBI34/hg16) [GRCh37/hg19]

Details

The locations of the cytogenetic bands in different builds of the human genome have been obtained from the Ensembl database using the MySQL commands listed on this page.

Output

The input file appended with a new column (cytoband) containing the name of the cytogenetic band (e.g. "8q24.21"). If the start and end positions are contained within different cytogenetic bands, the two bands are separated with a hyphen (e.g. "8q22.1-8q24.3").

References

Ensembl:
Flicek et al. (2010) Ensembl's 10th year. Nucleic Acids Res 38: D557