Samtools comand problem

[Firebird]

Hi,

I have a problem with the comand "view".
I only want to view 1 nukleotide, but when I write something like 1:100-100 I always get more than 1 base.

Is there an option for the "pileup" comand to show only one base?

Thanks!

[nilshomer]

Hi,

I have a problem with the comand "view".
I only want to view 1 nukleotide, but when I write something like 1:100-100 I always get more than 1 base.

Is there an option for the "pileup" comand to show only one base?

Thanks!

View will show all reads that overlap that base. You could use "grep" for finding the right line in your pileup.

[Firebird]

Thank you, but can you tell me the synthax for "grep".

[zee]

Thank you, but can you tell me the synthax for "grep".

I think this discussion is going way beyond samtools. Perhaps the following will work:

echo -e "1 100" > sites.txt
samtools view -u file.bam 1:100-100 | samtools pileup - -l sites.txt