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Kurt-Hetrick / CIDR_SEQ_CAPTURE_JOINT_CALL

CIDR exome and targeted resequencing joint calling/filtering pipeline
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switch to doing concordance on grch38 arrays #115

Open Kurt-Hetrick opened 4 months ago

Kurt-Hetrick commented 4 months ago

not sure about the best strategy at the moment. options to consider.

  1. new pipelines for every pipeline. not my favorite, but doable. mostly the submitters have to be new with a couple new scripts added to either build specific or common scripts.
  2. new branch, change the current one to a new branch and make the grch38 branch the main branch. probably less favorable than number 1 b/c of having to push/pull changes from branches to keep both of the current...probalby have to another branch specific dev branch as well. yeah, not doing this one after typing it down.
  3. add a new default switch/argument. one that specifies array build and then build an if/then statement calling specific functions for concordance workflow. can either make it optional and default it to a specific build or mandatory and validate that it is both present and specified in a specific way. this is probably the best option, but of course it would take the most amount of work/expertise. would have to start on it soon.
Kurt-Hetrick commented 2 months ago

for grch38 pipelines this is pretty straightforward. for grch37 pipelines, have to implement scatter gathering of the liftovers of the final vcf because doing it all at once runs into out of memory issues.

Kurt-Hetrick commented 1 month ago

done for grch38 pipelines (that have been created to date)