Re: [Samtools-help] Inferring stats from Bam File

[Henrikki A. <hen...@he...>]

Pratap, Abhishek wrote:
> Hi All
> 
> Sorry to push this out again. I am really looking to get few facts 
> straight about how to count stuff in bam file. I am not able to
> address the following questions.
> 
> 1. How do we know the #uniquely mapped reads in a bam file ? Will the
> following do the trick after subtracting from the total mapped reads
> ? samtools view -f 100 s_7_combined_sorted.bam | wc –l

I use following 'samtools view -F 0x0004 <file>' as that filters out the
non matching ones.

> 2. total #reads that mapped irrespective of whether they were paired
> or not ?

That's the line number of the read entries. So for example with regular
sam file 'cat <file> | egrep -v '^@' | wc -l' would count them.

> 3. 33501178 with itself and mate mapped  :  this comes from the
> samtools flagstat command but I dont get the meaning of "with itself
> "

-- 
Henrikki Almusa