Converts a BAM or CRAM into either FASTQ or FASTA format depending on the command invoked.
samtools fasta [options] in.bam
OPTIONS:
-n
By default, either '/1' or '/2' is added to the end of read names where the corresponding BAM_READ1 or BAM_READ2 flag is set. Using -n causes read names to be left as they are.
-O
Use quality values from OQ tags in preference to standard quality string if available.
-s FILE
Write singleton reads in FASTQ format to FILE instead of outputting them.
-t
Copy RG, BC and QT tags to the FASTQ header line, if they exist.
-1 FILE
Write reads with the BAM_READ1 flag set to FILE instead of outputting them.
-2 FILE
Write reads with the BAM_READ2 flag set to FILE instead of outputting them.
-0 FILE
Write reads with both or neither of the BAM_READ1 and BAM_READ2 flags set to FILE instead of outputting them.
-f INT
Only output alignments with all bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].
-F INT
Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0].