The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use bowtie2 (or BWA), instead. And a new config option could be created to switch between the different aligners that we offer.
As for the variant calling pipeline, we could update it to use VarCA and have it use different options when executing BWA. The only problem with using VarCA at the moment is that it doesn't output GQ tags, but issue #60 would resolve that.
aryarm
commented
3 years ago
The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use
bowtie2(orBWA), instead. And a new config option could be created to switch between the different aligners that we offer.As for the variant calling pipeline, we could update it to use VarCA and have it use different options when executing
BWA. The only problem with using VarCA at the moment is that it doesn't output GQ tags, but issue #60 would resolve that.