Troubleshooting

In case you have any issues, please check the previous issues on git and the Troubleshoot section of the DROP paper. If you have a new issue, please create a new one on git.

Common errors

The MAE:mae_allelicCounts step is susceptible to fail if:

1. the chromosomes styles of the reference genome and the BAM files do not match

Solution: Identify the chromosomes style of the BAM file. Obtain an appropriate reference genome file and specify it in the config file.

2. the BAM file does not have the correct Read Groups documentation both the header and reads. You can often identify if the BAM file has any problems by using the command gatk ValidateSamFile -I path/to/bam_file.bam

Solution: To fix this is often dependent on the individual case, but some combination of the following tools is quite helpful:

• samtools reheader
• gatk AddOrReplaceReadGroups