Test-drive the GATK tools and Best Practices pipelines on Terra
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Depth of Coverage - Only one type of output
I am using DepthOfCoverage for the first time
I used the following command to get the coverage and I am getting only one output file, which gives coverage per samples. I am giving gene list in REFSEQ format along with a sorted interval BED file. However I am not getting any file with per gene coverage.
Could anyone clarify whether I am missing something in the arguments
java -Xmx8g -jar GenomeAnalysisTK.jar -R Homo_sapiens_assembly19.fasta -T DepthOfCoverage --calculateCoverageOverGenes:REFSEQ Genes_refgene.txt --outputFormat table -o Coverage_summary -I BAM.list -L genes.bed