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Can I get each chromosomes offset ranges in Sorted BAM/SAM file

I am looking to get the offset ranges of the each chromosome from the sorted SAM/BAM file. Is it possible?

bam sam
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updated by venu venu • written by deepak643 • deepak643

what is "offset ranges " ? the file index (fseek ?) ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Yes the fseek to location in file. So in a sorted bam, the chromosome records will be from chr1 to chr25 sequentially. So I mean the offset ranges as chr1's records are from line number 1 to line 10. chr2 are from line 11 to line 20 and so on. So is there any way that I can get those offset ranges? Or else even knowing from which line chr2/chr3/.. starts will also help.

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written by deepak643 • deepak643

what devon said. You just need a BAI index to get some specific reads at a given location.

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written by Pierre Lindenbaum Pierre Lindenbaum

For indexed BAM files, this is available in the .bai index file. If you take the virtual file offset of the first bin of each chromosome, you should be able to >>16 that and get the file offset to the bin.

Edit: For SAM files, I suppose you could try tabix, but I'm not sure why one would want to do that.

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written by Devon Ryan Devon Ryan

is there any api or samtools command to get the virtual offset from bai file?

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written by deepak643 • deepak643

I don't think it's meant to be used (so it's not really documented), but presumably the hts_idx_t object from htslib would hold that.

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written by Devon Ryan Devon Ryan

1 answer

From your comment even knowing from which line chr2/chr3/.. starts will also help

I would do something like following

  • Create a file containing all the chromosome names, one per each line, say chr.txt

Using chr.txt, I would do

cat chr.txt | xargs -I {} grep -n {} foo.sam | sed 's/:/ /' | sort -k2 -u > chr_line_number.txt

head chr_line_number.txt

1  chr1
3  chr2
5  chr3
...
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written by venu venu

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