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'''Syntax''':
'''Syntax''':
baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v]
baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v] [-g or -R]
-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
-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
-s -> load SNP positions from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomevector (binary memory mapped file). For NCBI 37, a sample dbSNP file is located in /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl
-v -> output SAM record in which mismatched bases exist
-v -> output SAM record in which mismatched bases exist
-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 - '
Example:
Example:
