Is it possible to work on a part of a BAM file?
Since these files are huge, I want to extract 1MB of the BAM file and convert it to SAM.
My main intention is to extract a meaningful part from the BAM file and then convert it to SAM instead of converting the whole BAM file to SAM.
Thanks in advance for your answers.
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written
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User 9906 •
2 answers
It would help if you gave an idea of what you are trying to do with the BAM file. To extract a portion of the BAM file you could try something like
samtools view -h aln.sorted.bam chr2:20,100,000-20,200,000 > out.sam
to get reads from a region of the bam file. Or to get a certain number of reads you may try
samtools view aln.sorted.bam chr2:20,100,000-20,200,000 | head -20000 | samtools view -t ref.fa.fai - > out.sam
where ref.fa.fai is a tab delimited file generated using samtools faidx command. The above command will pick 20000 reads from the selected region.
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