The current version of the software is 1.8 and was last updated on Feb 9,2015. A copy of the current user guide for those interested in requirements and general information before agreeing to the download terms can be found here.

Frequently Asked Questions

What FASTQ file naming convention is Churchill expecting?
Churchill currently expects Read 1 of both Single End and Paired End data to use the convention *_R1.fastq* or *.R1.fastq* and Read 2 of Paired End data to use *_R2.fastq* or *.R2.fastq*.

Why does Churchill seem to be stuck on the “” script for a long time?
Make sure you have the ‘JOBS_PER_PACKAGE’ parameter set. It was erroneously marked as optional in the sample config. This is not the case and it needs to be set for all versions of Churchill. This parameter multi-threads the merging of the recalibration tables. In the Make and Shared version of Churchill, it should be set to the number of cores you have on the machine, or 1. This will be corrected in version 1.9.

Why is Churchill throwing an error regarding local variable 'BWA_TRIMMING_Q'?
This required parameter was left out of the sample config. For good quality Illumina data, it should be set to 0. If you have concerns about the quality at the end of your reads, you may set it to something higher (such as 15). This will be corrected in version 1.9.

Can I use the most recent version of BWA/Samtools/Picard/GATK/etc even though the User Guide specifies an older version?
We believe that newer versions of the software should work with Churchill, however the version specified in the User Guide is the latest one for which we have done extensive testing for that software component. Therefore, we would like users to be aware that unintended results, including failed runs, are possible when using versions other than those specified in the User Guide.

Further questions can be directed to