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Bam File: Extract Chromosome Number And Start Position Reads

Dear All,

I am working with BAM files for chip-seq analysis. For each read in the BAM file, I want to extractt the chromosome number, the start position and the stop position and replace that in a new file. Is that possible?

Many thanks!

bam samtools
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updated by Ram Ram • written by Lisanne • Lisanne

3 answers

samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

will do the job. The stop position here is the last matching position.

• 1 views • link
written by Farhat Farhat

Thanks to Farhat, that works fine for me! :)

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written by Lisanne • Lisanne

this approach has a minor issue that the length of the sequence does not necessarily agree with the span of the alignment, e.g. indels

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written by Wen.Huang Wen.Huang

bedtools' bamToBed inspects the CIGAR string when computing the end coordinate, so deletions are properly handled. the example here assumes that only substitutions can occur,

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written by Aaronquinlan Aaronquinlan

True. bamToBed would be the proper tool to handle something like this.

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written by Farhat Farhat

Yes it is pssible, using e.g. SAMtools samtools view or Rsamtools.

The reference sequence name is in column 3 of a SAM file, the (leftmost) start in column 4 and the end position needs to be calculated using the CIGAR string (e.g. start + alignment length).

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written by Michael Dondrup Michael Dondrup

In this case how is strand information treated? Is it always start + alignment length or does it depends on the strand where the read mapped?

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updated by Ram Ram • written by mjg • mjg

You could also try BEDTools, which can convert your .bam to a .bed, and bed pretty much is a name, a chromosome, a start and a stop position.

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updated by Ram Ram • written by Swbarnes2 Swbarnes2

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