grenepipe
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moiexpositoalonsolab
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
Hi After editing the reference genome file, as you suggested, it worked for individual sample files but there is still a problem with PoolSeq data . It crashed and the...
(grenepipe) [sysu_mhwang_1@sy3ubuntu1804-23101937-698d4864d-99fwt envs]$conda install mamba Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry...
Hello, I've been looking around at published complete variant calling pipelines, and grenepipe seems both high quality and very flexible. It would be nice if there were the option to...
Hi Lucas, I wish to call specific sites and have found that using the `restrict-regions` option to indicate a intervals.bed file specifying those sites works for this purpose (in combination...
Hello, I had a first look to grenepipe and first, thanks for a handy tool. Would it be possible to make the "trimming-tool" step optional please ? Currently, valid values...
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A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.