Thank you :)
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clear.choi •
Extract Fastq file from BAM File by reference name using samtools.
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!
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Ram
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clear.choi •
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clear.choi •
1 answer
It might help if you clarify your question, but I think you want:
samtools view -f 0 -r B3 -b -o out.bam in.bam A_01_01
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Ram
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Matt Shirley
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