change code to use max_coverage, calc mean coverage and set max coverage to something 3sigma above the mean
***first new feature they'd really like to see (updatRef.pl update parental genome line 204 $t pileup file col 7 is num of reads that map to that genetic location
Samtools pileup format, new format they use puts it in column 7
if > min and not all 0 in quality and less than mean + 3std dev then update the site.
if not then N the base out
property update_minQV=0 ignore pileups if >0 will mask regions not updated
Confirm col 7 is the correct number.
Calc mean from sites covered not from whole genome
Misc. Meeting notes:
change code to use max_coverage, calc mean coverage and set max coverage to something 3sigma above the mean ***first new feature they'd really like to see (updatRef.pl update parental genome line 204 $t pileup file col 7 is num of reads that map to that genetic location Samtools pileup format, new format they use puts it in column 7 if > min and not all 0 in quality and less than mean + 3std dev then update the site. if not then N the base out property update_minQV=0 ignore pileups if >0 will mask regions not updated Confirm col 7 is the correct number. Calc mean from sites covered not from whole genome