How to convert complete bam to mpileup

[Seq_g]

Hey,
While doing mpileup, I could see that lot of reads are not counted in mpileup output although I could see them in tview,
I am using following command:

samtools mpileup -d 10000 -f Ref.fasta accepted_hits.bam > mpileup

(BTW: I have this problem in all coverage, so its not because of -d flag)

I understood from this link that in samtools tview underlined reads are orphan therefore not counted in mpileup. Is there any way NOT to consider any parameter but to get the complete count at each site

Thank you very much

[dariober]

Hey,
I understood from this link that in samtools tview underlined reads are orphan therefore not counted in mpileup. Is there any way NOT to consider any parameter but to get the complete count at each site

Thank you very much

Hi- A work around this is to remove the flags that mpileup discards from the input bam. For example orphan reads should be those with flag 8 which means mate unmapped (see also http://picard.sourceforge.net/explain-flags.html). This could be done with a fairly simple script in your favourite language (maybe there are off-the-shelf tools to edit sam flags?).

In my opinion it would be very useful if mpileup would let the user choose which reads include and exclude (the other day I found out that also reads marked as duplicate are automatically discarded).

Dario