255
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
'''Base Quality Check'''
'''Base Quality Check'''
'''(May 11, 2010 - Paul, Xiaowei)'''
'''(Aug 27, 2010 - Paul, Xiaowei)'''
'''Syntax''':
'''Syntax''':
baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R]
baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R] [-2]
-c -> only process first (max record count) of alignment.
-c -> only process first (max record count) of alignment.
-q -> alignment with less than minimum mapping quality will not be counted
-q -> alignment with less than minimum mapping quality will not be counted
-g -> output in GNU Plot code, you can pipe the output using '|gnuplot'
-g -> output in GNU Plot code, you can pipe the output using '|gnuplot'
-R -> output in R code, you can pipe the output using '|Rscript --vanilla - '
-R -> output in R code, you can pipe the output using '|Rscript --vanilla - '
-2 -> use SNP position for color space reads
Example:
Example:
Check first 20000 lines of abc.sam, using /data/local/ref/karma.ref/human.g1k.v37.fa as reference genome, excluding SNP sites specified in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
Check first 20000 lines of abc.sam, using /data/local/ref/karma.ref/human.g1k.v37.fa as reference genome, excluding SNP sites specified in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
