gsMapper contigs

[haonmada]

Hello All,

What does the lower case and upper case Letters in the contigs build by gsMapper represent?

Also, How is HCDiff (high confidence) variations differences determined?

Thanks
HA

[jjohnson]

Hi Ha,

The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants that have at least 3 non-duplicate reads relative to the reference or to other reads at that specific location.

I also found another thread that discusses uppercase and lower case and maybe helpful.

http://seqanswers.com/forums/showthread.php?t=1948