Hi Dror,
that's unexpected, I cannot think of a reason why that should be so,
other than a bug. Would you mind sending some debugging info? For
example, you could do:
samtools view test.bam | awk '{print and($2,0x4)}' | sort | uniq -c
and if that does not reveal anything, could you send us qualities from
all three outputs (samtools view ... | cut -f2 | gzip -c > out.gz )?
Thanks,
petr
On Sun, 2014-08-31 at 13:17 +0300, Dror Hibsh wrote:
> Hi,
> I dont understand what is the difference between these options:
>
>
> 1. samtools view file.bam
>
> 2. samtools view -F 4 file.bam
>
> 3. samtools view -f 4 file.bam
>
>
>
> i used it on a bam file and i got these results (respectively):
> 1. 841903259
>
> 2. 817892859
>
> 3. 24381062
>
>
>
> I thoght that:
> -F is only the mapped reads
> -f is only the unmapped reads
> and only 'view' will print both.
>
>
> So, i would expect to have:
> 817892859+24381062 will be equal to 841903259
>
> but option 2 + 3 doesnt equal to option 1.
>
>
> Can you pls explain what i dont understand?
>
>
>
>
> Plus, what will be the difference if i will use:
> samtools view -s 0.2 file.bam 1:0-5000000
>
> As far as i understand, i will get only the mapped reads (as the -F 4
> option), but for the specific region.
>
>
> Thanks,
> Dror
>
>
>
>
>
>
> --
> -----------------
> Dror Hibsh
> 0507-669599
> ------------------
>
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