Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R reference.fasta -I input.bam -o output.bam -U ALLOW_N_CIGARS


Manual

Argument name(s)Default valueSummary
Optional Outputs
--out
 -o
stdoutWrite output to this BAM filename instead of STDOUT
Optional Flags
--doNotFixOverhangs
falsedo not have the walker hard-clip overhanging sections of the reads
Advanced Parameters
--maxBasesInOverhang
 -maxOverhang
40max number of bases allowed in the overhang
--maxMismatchesInOverhang
 -maxMismatches
1max number of mismatches allowed in the overhang
--maxReadsInMemory
 -maxInMemory
150000max reads allowed to be kept in memory at a time by the BAM writer


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