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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]
-c -> only process first (max record count).
-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
-r -> reference genome (in KARMA format)
-r -> reference genome (in KARMA format)
-v -> output SAM record in which mismatched bases exist
-v -> output SAM record in which mismatched bases exist
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
baseQualityCheck -c 20000 -r /data/local/ref/karma.ref/human.g1k.v37.fa -s /home/bingshan/data/db/dbSNP130.UCSC.coordinates.tbl abc.sam
Thank '''Bingshan''' for his qPlot program and his input to finish this program.
Thank '''Bingshan''' for his qPlot program and his input to finish this program.
