Question: Problem With Depth Of Coverage On Bam Files (Gatk Tools)
0
Lilach F • 190 wrote:
Hi,
I am trying to used Depth of Coverage to see the coverages is specific
intervals.
The intervals were taken from UCSC (exons of 2 genes), loaded to
Galaxy and
the file type was changed to intervals.
I gave to Depth of Coverage two BAM files (resulted from BWA,
selection of
only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM)
and the intervals file (in advanced GATK options).
The consensus genome is hg_g1k_v37.
I got the following error message:
An error occurred running this job: *Picked up _JAVA_OPTIONS:
-Djava.io.tmpdir=/space/g2main
##### ERROR
##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0):
##### ERROR The invalid argume
*Is it a bug, or did I do anything wrong?
I will be grateful for any help.
Thanks!
Lilach*
*
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modified 6.5 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
6.5 years ago by
Lilach F • 190