Does anybody know how to get gene coverage from targeted exome sequencing?
I would like to compute the coverage of a target reference using an aligned exome sample. I want the coverage both for exome and for gene.
Thanks
For genes I could do it, thanks. What shall I do to make it for exons?
Got to http://genome.ucsc.edu
Click "Tools" and "Table browser". Group: Genes and Gene Predictions. Track: Refseq Genes. Table: Refgene. Output format: BED - browser extensible data. Give an Output File name. Click "Get Output", then select either Exons plus (and some overhang at each end), or if you want to ignore UTR and non-coding transcripts, select "Coding exons". Then Get BED.
So that file then I have to use as gene list right?
java -Xmx64g -jar GenomeAnalysisTK.jar
-T DepthOfCoverage
-R ucsc.hg19.fa
-I file.bam
-L target_file.interval_list
-geneList refSeq.txt
-ct 10 -ct 20 -ct 40 -ct 80
-o output
Thanks
Hi Francesco,
I haven't actually tried doing this myself, but the GATK help does say that the ROD files (genelists) can be in bed format, so my suggestion might work. The following help guides may (or may not) be useful!
https://www.broadinstitute.org/gatk/guide/article?id=1329
http://gatkforums.broadinstitute.org/gatk/discussion/1204/what-input-files-does-the-gatk-accept-require
Good luck! :)
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