Insert Size For Each Bam Entry

Question

[Nicolas Rosewick]

Hi,

I've a bam file and I want to know the insert size for each entry. I know that picard CollectInsertSizeMetrics gives me statistics about insert size, but is it possible to have it for every entry ?

thanks

Answer 1

[Ashutosh Pandey]

The ninth column of the SAM file (TLEN) approximately represents the insert size. Subtract length of a read (For example 75 bp or 100 bp) from TLEN to get the insert size.

See this earlier post from me:

estimating Insert size from paired end data.

[seta]

I know I'm late. But, given the information at http://thegenomefactory.blogspot.de/2013/08/paired-end-read-confusion-library.html, are you sure about subtracting?

Answer 2

[Vitis]

Please see Bio::DB::Sam perl API for accessing SAM and BAM files. It has an explicit function to fetch the insert size for each mapped read pair. http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm#BAM_Files