From e5175aaeb1cf77ec26654627757c521fd1cc51ab Mon Sep 17 00:00:00 2001 From: Kishwar Date: Tue, 2 Nov 2021 20:11:41 -0700 Subject: [PATCH] r0.6 readme updates --- README.md | 42 ++++++++++++------- docs/pipeline_docker/ONT_variant_calling.md | 2 +- .../ONT_variant_calling_singularity.md | 2 +- 3 files changed, 28 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index ede115e9..c2d60dd1 100644 --- a/README.md +++ b/README.md @@ -11,10 +11,10 @@ ### Version 0.6 update PEPPER-Margin-deepvariant v0.6 supports: -* Oxford Nanopore Variant calling for Guppy 5.0.7 "Sup" basecaller -* Oxford Nanopore Variant calling for R10.4 Q20 -* PacBio-HiFi data - +* Oxford Nanopore Variant calling for Guppy 5.0.7 "Sup" basecaller. +* Oxford Nanopore Variant calling for R10.4 Q20. +* PacBio-HiFi variant calling. +* Assembly-based structural variant calling method [HapDup](https://github.com/fenderglass/hapdup). --- ### How to cite @@ -23,19 +23,28 @@ Please cite the following manuscript if you are using `PEPPER-Margin-DeepVariant
Nature Methods: Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks. -Authors: Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel,
Gunjan Baid, Jordan M Eizenga, Karen H Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten. +Authors: Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel,
Gunjan Baid, Mikhail Kolmogorov, Jordan M. Eizenga, Karen H. Miga, Paolo Carnevali, Miten Jain, Andrew Carroll & Benedict Paten.
--- -### Quickstart -Please follow the quickstart guides to assess your setup. Please follow case-study documentations for detailed instructions. -#### Oxford Nanopore -* **Docker**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_docker_quickstart.md). -* **Singularity**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_singularity_quickstart.md). - -#### PacBio-HiFi -* **Docker**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_docker_quickstart.md). -* **Singularity**: [Oxford Nanopore variant calling quick start](./docs/quickstart/variant_calling_singularity_quickstart.md). +### How to run +PEPPER-Margin-DeepVariant can be run using **Docker** or **Singularity**. A simple docker command looks like: +```bash +sudo docker run \ +-v "${INPUT_DIR}":"${INPUT_DIR}" \ +-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \ +kishwars/pepper_deepvariant:r0.6 \ +run_pepper_margin_deepvariant call_variant \ +-b "${INPUT_DIR}/${BAM}" \ +-f "${INPUT_DIR}/${REF}" \ +-o "${OUTPUT_DIR}" \ +-t "${THREADS}" \ +--ont_r9_guppy5_sup + +# --ont_r9_guppy5_sup is preset for ONT R9.4.1 Guppy 5 "Sup" basecaller +# for ONT R10.4 Q20 reads: --ont_r10_q20 +# for PacBio-HiFi reads: --hifi +``` ### Case studies @@ -45,10 +54,11 @@ The variant calling pipeline can be run on [Docker](https://docs.docker.com/inst The case-studies include input data and benchmarking of the run: * Nanopore variant calling using **Docker**: [Link](./docs/pipeline_docker/ONT_variant_calling.md) * Nanopore variant calling using **Singularity**: [Link](./docs/pipeline_singularity/ONT_variant_calling_singularity.md) +* **Nanopore R10.4 Q20** variant calling: [Link](./docs/pipeline_docker/ONT_variant_calling_r10_q20.md) #### PacBio-HiFi variant calling -* Nanopore variant calling using **Docker**: [Link](./docs/pipeline_docker/ONT_variant_calling.md) -* Nanopore variant calling using **Singularity**: [Link](./docs/pipeline_singularity/ONT_variant_calling_singularity.md) +* PacBio-HiFi variant calling using **Docker**: [Link](./docs/pipeline_docker/HiFi_variant_calling.md) +* PacBio-HiFi variant calling using **Singularity**: [Link](./docs/pipeline_singularity/HiFi_variant_calling_singularity.md) ### License [PEPPER license](./LICENSE), [Margin License](https://github.com/UCSC-nanopore-cgl/margin/blob/master/LICENSE.txt) and [DeepVariant License](https://github.com/google/deepvariant/blob/r1.1/LICENSE) extend to the trained models (PEPPER, Margin and DeepVariant) and container environment (Docker and Singularity). diff --git a/docs/pipeline_docker/ONT_variant_calling.md b/docs/pipeline_docker/ONT_variant_calling.md index 03e1e28f..7c97c2c6 100644 --- a/docs/pipeline_docker/ONT_variant_calling.md +++ b/docs/pipeline_docker/ONT_variant_calling.md @@ -100,7 +100,7 @@ run_pepper_margin_deepvariant call_variant \ -f "${INPUT_DIR}/${REF}" \ -o "${OUTPUT_DIR}" \ -t "${THREADS}" \ ---ont_r9_guppy5_sup # For R10.4 Q20 reads set: --ont_r10_q20 +--ont_r9_guppy5_sup ``` ###### Evaluation using hap.py (Optional) diff --git a/docs/pipeline_singularity/ONT_variant_calling_singularity.md b/docs/pipeline_singularity/ONT_variant_calling_singularity.md index 4e593fc4..aea34952 100644 --- a/docs/pipeline_singularity/ONT_variant_calling_singularity.md +++ b/docs/pipeline_singularity/ONT_variant_calling_singularity.md @@ -10,7 +10,7 @@ We evaluated this pipeline on `~30x` HG002 data. ```bash Sample: HG002 Coverage: ~25-90x -Basecaller: Guppy 5.0.7 or higher +Basecaller: Guppy 5.0.7 SUP or higher Region: chr20 Reference: GRCh38_no_alt ```