pileup only on a specific position

[foxyg]

I am wondering is there a way to use samtools pileup to out put pileup only on 1 position I want? Since the bam file is sorted and indexed, I would think this is doable, I saw there is a -l option for pileup, but couldn't make it work. Does anyone know how?

Thanks

[drio]

I assume you want to do it based on the coordinates?

$ samtools view my.bam | awk '$3=="chr1" && $4>5 && $4<10'

That will show you the positions for chr1 where the coordinates are >5 and <10.

[krobison]

You can also supply a set of positions in a space delimited file with the -l option

samtools pileup -l site-list.txt my.bam myref.fa

where site-list.txt might contain

chr1 123456789

[foxyg]

Both of those method works sort of, but the problem is they don't stop after I found what I wanted. For example if I only want the 1 position in chr1, it will still search through the whole bam file, which is wasting a lot of time.

[lh3]

samtools mpileup -r chr1:100-100 ...

[liux]

samtools mpileup -r chr1:100-100 ...

this is very nice feature. But it seems that it can only output one region at a time？

I am wondering if the pileup can be made according to a BED file or any files that defines a series of regions. It is particularly useful for targeted exome re-sequencing.

[lh3]

speed-wise, taking a BED or not will not make a big difference. The speed of mpileup is determined by the number of reads. As the majority of reads fall in targeted regions, time spent on non-target regions is relatively small.

[liux]

In my case (maybe very special), there are a couple dozen out of all genes are of interests. so, to output only the specific exons is often requested.

[genesquared]

Hi there,

I have similar question too.

samtools view ftp://hgdownload.cse.ucsc.edu/gbdb/h...33.16.hg18.bam chr3:36186433-36186433

give me a short sequence w multiple bps, instead of 1 bp that I prefer.

& my Window PC does not have the "awk" function

Thanks in advance.