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
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Dror Hibsh
0507-669599
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