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Revision as of 12:06, 6 February 2012
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= Usage =
= Usage =
./bam indelDiscordance --in <inputFile> [--bamIndex <bamIndexFile] [--refFile <filename>] [--umRef] [--depth minDepth] [--minRepeatLen len] [--sumRepeatLen len] [--printPos] [--chrom <name>] [--start 0basedPos] [--end 0basedPos] [--noeof] [--params]
= Parameters =
= Parameters =
--sumRepeatLen : all repeats this length and longer will be accumulated,
--sumRepeatLen : all repeats this length and longer will be accumulated,
DEFAULT = 5
DEFAULT = 5
--avgDepthMult : max depth used is the average depth * this multiplier,
DEFAULT = 3
--printPos : print details for each position
--printPos : print details for each position
--printCounts : print counts of occurrances of each repeat count and of discordant cigars for each repeat count
--sample : output the specified sample name as part of the error rate/depth table
--gender : output the specified gender as part of the error rate/depth table
--chrom : chromosome name other than X
--chrom : chromosome name other than X
--start : use a 0-based inclusive start position other than the default, 2699520
--start : use a 0-based inclusive start position other than the default, 2699520
