The current GATK version is 3.5-0

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

# DepthOfCoverage (without -L option) output

ItalyPosts: 3Member

Hi there!
I tried to analyse the depth of coverage of my exome data using GATK DepthOfCoverage

java -Xmx${heap}m \ -Djava.io.tmpdir=$processed_bam/tmp_folder_dept \
-jar $gatk \ -T DepthOfCoverage \ -omitBaseOutput \ -omitLocusTable \ -R$GRCh37_ref_WholeGenome \
-I $file \ -o$coverage/\${samplename}.coverage.dept

I am not interested in particular genomic regions, so I haven't a target list file.
How were the intervals determined in "_interval_statistics" output file?
Where can I obtain an interval target list file including all exons in the human genome?
Thank you very much!

Fulvio

Tagged:

• ItalyPosts: 3Member

I think if I set -omitIntervals -omitBaseOutput -omitLocusTable options, I'll obtain no results, isn't it?

I'm not interested in specific intervals, but I would obtain a coverage for all exons. Could it fuction using for the -L option an exon list in bed format downloaded from UCSC?

Don't you know what are the intervals generated in that "_interval_statistics" output?
Source_of_reads from_0_to_1) from_1_to_2) from_2_to_3) from_3_to_4) ...

Thanks!

Fulvio

• ItalyPosts: 3Member

Ah, ok! It does not matter, It was only a curiosity! However the generated intervals are

 from_0_to_1) ... from_500_to_inf


so they don't correspond to chromosomes.

Best regards!

Fulvio