Hello Lilach,

More documentation for the beta GATK tools is coming soon, but meanwhile here is some help.

To adjust the "Depth Of Coverage" form to count at the base level:

Scroll down on the tool form and set Advanced GATK Options --> Advanced. This will reveal a new set of options: "Operate on Genomic intervals". You an add/exclude interval ranges and set rules. Input types are "bed,gatk_interval,picard_interval_list,vcf".

To set the genome:

Locate the same genome as you used for the BWA alignment, then follow these instructions to use a Custom reference genome (only one genome is set up to be used natively, while the tool is in beta).
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

The option to to use a Custom reference genome is at the top of the tool form: "Choose the source for the reference list:". Set this to "History". Then mid-way down, set "Using reference genome:" to be the genome in fasta format as a dataset in your history.

Best,

Jen
Galaxy team

On 4/2/12 8:39 AM, Lilach Friedman wrote:
and another question:
My steps were:
1. BWA alignment
2. SAM-to-BAM
3. rmdup.

when I'm trying to give 3 (rmdup results) as an input to GATK
DepthOfCoverage, an error appears: "
Sequences are not currently available for the specified build."

What did I do wrong?

Many thanks!
    Lilach

2012/4/2 Lilach Friedman <lilac...@gmail.com <mailto:lilac...@gmail.com>>

    Hi,

    I have NGS results of DNA enriched for exons with an AllExon kit
    (Agilent).
    I have a bed file with the list of targeted sequences.
    I want to use GATK DepthOfCoverage to compare the results to the bed
    file and to get all the targets that were covered by <n reads.

    How can I do that with Galaxy on the web? or in Amazon?

    My question has 2 parts:
    1. How can I specify the target intervals in Galaxy on the web?
    (the "-L" command in Unix commandline)
    2. How can I ask the coverage for single bases instead of statistics?


    Thanks,
        Lilach



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