USing GATK DepthOfCoverage with all exon enriched data
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
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 <lilachfr@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
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 <lilachfr@gmail.com <mailto:lilachfr@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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
participants (2)
-
Jennifer Jackson
-
Lilach Friedman