From 5e95f1710058e5c000670df21a72d666cf3e0d61 Mon Sep 17 00:00:00 2001 From: shafin Date: Tue, 3 Dec 2024 20:47:27 -0800 Subject: [PATCH] Fix typos and doc formatting PiperOrigin-RevId: 702568997 --- README.md | 9 ++++----- docs/trio-merge-case-study.md | 22 ++++++++++------------ 2 files changed, 14 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 7e1ff828..a592b85f 100644 --- a/README.md +++ b/README.md @@ -41,7 +41,7 @@ DeepVariant supports germline variant-calling in diploid organisms. [Mapped with BWA](docs/pangenome-aware-wes-bwa-case-study.md). We have also adapted DeepVariant for somatic calling. See the -[github.com/google/deepsomatic](DeepSomatic) repo for details. +[DeepSomatic](https://github.com/google/deepsomatic) repo for details. Please also note: @@ -113,13 +113,12 @@ To see all flags you can use, run: `docker run google/deepvariant:"${BIN_VERSION}"` If you're using GPUs, or want to use Singularity instead, see -[Quick Start](docs/deepvariant-quick-start.md) for more details or see all the -[setup options](#deepvariant_setup) available. +[Quick Start](docs/deepvariant-quick-start.md) for more details. If you are running on a machine with a GPU, an experimental mode is available that enables running the `make_examples` stage on the CPU while the `call_variants` stage runs on the GPU simultaneously. -For more details, refer to the [Fast Pipelione case study](docs/deepvariant-fast-pipeline-case-study.md). +For more details, refer to the [Fast Pipeline case study](docs/deepvariant-fast-pipeline-case-study.md). For more information, also see: @@ -205,7 +204,7 @@ post on ### Prerequisites * Unix-like operating system (cannot run on Windows) -* Python 3.8 +* Python 3.10 ### Official Solutions diff --git a/docs/trio-merge-case-study.md b/docs/trio-merge-case-study.md index b4a3e375..e56bf58f 100644 --- a/docs/trio-merge-case-study.md +++ b/docs/trio-merge-case-study.md @@ -262,12 +262,11 @@ do done ``` -| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st | -: : : : : ALT) : ALT) : ALT) : -| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- | -| HG002 | 29955 | 11693 | 2.56 | 29942 | 11673 | 2.57 | -| HG003 | 29852 | 11769 | 2.54 | 29842 | 11746 | 2.54 | -| HG004 | 30048 | 11838 | 2.54 | 30037 | 11821 | 2.54 | +| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st ALT) | [7]tv (1st ALT) | [8]ts/tv (1st ALT) | +| ------ | ----- | ----- | -------- | --------------- | --------------- | ------------------ | +| HG002 | 29955 | 11693 | 2.56 | 29942 | 11673 | 2.57 | +| HG003 | 29852 | 11769 | 2.54 | 29842 | 1174 | 2.54 | +| HG004 | 30048 | 11838 | 2.54 | 3003 | 11821 | 2.54 | If you want to restrict to the truth BED files, use this command: @@ -287,12 +286,11 @@ done Which resulted in this table: -| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st | [7]tv (1st | [8]ts/tv (1st | -: : : : : ALT) : ALT) : ALT) : -| ------ | ----- | ----- | -------- | ---------- | ---------- | ------------- | -| HG002 | 27716 | 10549 | 2.63 | 27708 | 10536 | 2.63 | -| HG003 | 27382 | 10527 | 2.60 | 27378 | 10515 | 2.60 | -| HG004 | 27503 | 10607 | 2.59 | 27496 | 10596 | 2.59 | +| Sample | [3]ts | [4]tv | [5]ts/tv | [6]ts (1st ALT) | [7]tv (1st ALT) | [8]ts/tv (1st ALT) | +| ------ | ----- | ----- | -------- | --------------- | --------------- | ------------------ | +| HG002 | 27716 | 10549 | 2.63 | 27708 | 10536 | 2.63 | +| HG003 | 27382 | 10527 | 2.60 | 27378 | 10515 | 2.60 | +| HG004 | 27503 | 10607 | 2.59 | 27496 | 10596 | 2.59 | ### Rtg vcfstats