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support:hpc:software:bam2fasta

BAM2FASTA

BAM2FASTA

Usage: bam2fastq [options] <bam file>

OPTIONS

 
-o FILENAME, --output FILENAME
Specifies the name of the FASTQ file(s) that will be generated. May contain the special characters % (replaced with the lane number) and # (replaced with _1 or _2 to distinguish PE reads, removed for SE reads). [Default: s_%#_sequence.txt]
-f, --force, --overwrite
Create output files specified with --output, overwriting existing files if necessary [Default: exit program rather than overwrite files]
--aligned
--no-aligned
Reads in the BAM that are aligned will (will not) be extracted. [Default: extract aligned reads]
--unaligned
--no-unaligned
Reads in the BAM that are not aligned will (will not) be extracted. [Default: extract unaligned reads]
--filtered
--no-filtered
Reads that are marked as failing QC checks will (will not) be extracted. [Default: extract filtered reads]
-q, --quiet
Suppress informational messages [Default: print messages]
-s, --strict
Keep bam2fastq's processing to a minimum, assuming that the BAM strictly meets specifications. [Default: allow some errors in the BAM] 
support/hpc/software/bam2fasta.txt · Last modified: 2012/02/08 16:18 by tlknight