Genome Variant Analysis


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


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

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