arq5x/gemini — pull request #29 by chapmanb (2012-06-22 19:59:51+00:00)
Title: Mappability annotations: GMS and GRC

Aaron;
This adds annotations associated with mappability. The Genome Mappability Score (GMS) adds low GMS scores for Illumina, SOLiD and IonTorrent technologies derived from:

http://sourceforge.net/apps/mediawiki/gma-bio/index.php?title=Download_GMS#Download_GMS_by_Chromosome_and_Sequencing_Technology

This is generated by parsing the raw GMS inputs, filtering by GMS scores < 25.0 in any technology, and converting into a VCF input.

The GRC is a BED file of patched and fixed regions from the Genome Reference Consortium:

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/

The general notion is that variants falling into low mappability regions or GRC fix regions could be worth additional investigation for technology or genome specific errors.

Is there a good place to document the values and input file information?

Thanks for taking a look and let me know if you have any questions.