insert size via bamtools stats inner or outer ?
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6.6 years ago
Siva ▴ 20

Hi guys, 

I've a doubt about the meaning of "insert size" from bamtools stats.
I've done this : "bamtools stats -in $1 -insert" input is a bam produced with read1.fastq and read2.fastq (bwa), in each file reads' length is 100 b

and got an insert size of 241 so i supposed it's outer size = R1+R2+insert 

 

**********************************************
Stats for BAM file(s):
**********************************************
Total reads:       820130832 ...

Average insert size (absolute value): 309.402
Median insert size (absolute value): 241

 

Advance thanks, 

Siva

bamtools insert stat • 3.0k views
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6.6 years ago

test it:

 

// if the alignment is downstream of mate then you can get the end position of the read.

if(al.Position > al.MatePosition){

int outter = abs(al.MatePosition - al.GetEndPosition());

int inner = al.InsertSize;

if(outter != inner){

cerr << "insert length is inner" << end;

}

 

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