Large empty data using Depthofcoverage

Question

[mauro.castagnetta]

Dear all,

I'm trying to use DepthofCoverage tool on a bam file deriving from (IonTorrent obtained) fastq aligned using bwa.

I'm using my .refseq file which is converted from .bed file and it contains my genes of interest, they are 12 genes with several exons.

I'm obtaining after about 72h of analysis (on a core i7 and 16 gb of ram) only a huge sequence of zeros, zero intervals, zero coverage etc. etc.

Can anyone give me some advice?

Thanks in advance,

M

[Irsan]

Do you mean the DepthOfCoverage-walker of the Genome analysis tool kit (GATK)? If so, it helps when you give the exact command you used and it helps even more when you have any log-messages.

[mauro.castagnetta]

Yes, I was referring to DepthOfCoverage-walker from gatk2. I'm using it under Galaxy..

This is what I obtain from logs:

and to clarify, the data I've obtained are here:

http://pastebin.com/cypy96Fc

(only a small part...continue for several GBs..)

Thanks!

Mauro

Answer 1

[Irsan]

It appears as if you haven't told the DepthOfCoverage tool to restrict the analysis to you genes of interest. So what happens is that you get depth of coverage for the complete genome which in your case is most likely 0 for most of the genome. In the log-file you provided you can see a list of paramaters that you have set for the analysis (after: Program Args:). There should be something like -L /path/to/yourfileofinterest or --intervals /path/to/yourfileofinterest. I think your first problem right now is how to a compatible (Picard-style) interval-list file. You can have a look in the GATK documentation for more information.