Hi Everyone, Recently, I tried to use GATK - Depth of Coverage tool with my own .bam file on Galaxy for the first time. However it gave following error for each output. (see screenshot)
Depth of Coverage on data 4 and data 1 (output cumulative coverage proportions sample) error: An error occurred with this dataset: /bin/sh: 1: samtools: not found Traceback (most recent call last): File "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 126, in if __name__=="__main__": __main__() File "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 9
I searched the mailing list, but I couldn't find similar problem that posted before. How can I solve it? Should I install GATK seperately on Galaxy? or anything else? Can Holyavkin PhD Student Istanbul Technical University Molecular Biology and Genetics Dept.