Using Gatk Depthofcoverage With All Exon Enriched Data

Question: Using Gatk Depthofcoverage With All Exon Enriched Data

6.7 years ago by

Lilach F • 190

Lilach F • 190 wrote:

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<="" div="">

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modified 6.7 years ago • written 6.7 years ago by Lilach F • 190

6.7 years ago by

Lilach F • 190

Lilach F • 190 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>

ADD COMMENT • link written 6.7 years ago by Lilach F • 190

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 -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

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