Pileup file error

Question

[Sureshkumar V.]

Hi, I am working on the genome assembly. A sequence length 1216bp. Reads fully mapped on that region. When I am creating pileup file using samtools, I got only 1034bp.

How to clarify this problem?

Thanks in advance

Answer 1

[Devon Ryan]

There are default values for filtering reads and bases that are presumably affecting what you're seeing. Try -d 80000 -Q 1, possibly with -a -a if you want to be sure.

Note that you might also need to tweak --rf and --ff, though really the defaults should be kept.

[Sureshkumar V.]

Sir, When I saw using IGV. The Variant Positions has mapped to reads. I followed your parameters to make pileup file. I got the result, but It shows 0 reads in the position.

Why does it show like this?

[Devon Ryan]

Try -Q 0 then, it's a filtering criterion that's preventing you from seeing it. Note that criteria are there for a very good reason, so it's likely that the variant isn't real.