Hello,
I am trying to understand how to use samtools, and there is a little bit confusion.
I have one .BAM file which is 96 index is existed.
I can extract that specific index like below
samtool view -r B3 -b -o out.bam in.bam
[Ref: Extract Bamfile using samtools]
But I wonder if I want to use also Reference Name (fg, Reference name: A_01_01
)
And Flag which is contain 0 or 16. (0 mean Forward sequence and 16 mean Reverse sequence)
If I want to extract reference A_01_01
and Flag 0, what is exactly command line I can use?
After that I can extract to fastq file using below command.
samtools bam2fq output.bam > output.fastq
Thank you!
I really like samtools, but the flag notation is just so confusing to most people.
-f 0
will not work at all!! You want-F 16
Thank you :)