From 9a58167b5b6a6f2eeca39b20b1314e9015d562b3 Mon Sep 17 00:00:00 2001 From: jonbrenas Date: Sun, 15 Mar 2026 19:21:17 +0000 Subject: [PATCH 1/2] Updated VUGs --- docs/af1/af1.1.ipynb | 6 +++--- docs/af1/af1.2.ipynb | 6 +++--- docs/af1/af1.3.ipynb | 6 +++--- docs/af1/af1.4.ipynb | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/af1/af1.1.ipynb b/docs/af1/af1.1.ipynb index 4326bb1..05eb4ab 100644 --- a/docs/af1/af1.1.ipynb +++ b/docs/af1/af1.1.ipynb @@ -68,7 +68,7 @@ "source": [ "## Whole-genome sequencing and variant calling\n", "\n", - "All samples in `Af1.1` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " + "All samples in `Af1.1` (except for the samples in 1236-VO-TZ-OKUMU-VMF00248 and the samples in small-2020-af) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00248 ahve been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " ] }, { @@ -1256,9 +1256,9 @@ }, "environment": { "kernel": "mgenv_7.2.0", - "name": "workbench-notebooks.m138", + "name": "workbench-notebooks.m139", "type": "gcloud", - "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139" }, "kernelspec": { "display_name": "Python (mgenv_7.2.0)", diff --git a/docs/af1/af1.2.ipynb b/docs/af1/af1.2.ipynb index a826001..91f5728 100644 --- a/docs/af1/af1.2.ipynb +++ b/docs/af1/af1.2.ipynb @@ -57,7 +57,7 @@ "source": [ "## Whole-genome sequencing and variant calling\n", "\n", - "All samples in `Af1.2` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " + "All samples in 1281-VO-CM-CHRISTOPHE-VMF00227 have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00252 have been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " ] }, { @@ -685,9 +685,9 @@ }, "environment": { "kernel": "mgenv_7.2.0", - "name": "workbench-notebooks.m138", + "name": "workbench-notebooks.m139", "type": "gcloud", - "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139" }, "kernelspec": { "display_name": "Python (mgenv_7.2.0)", diff --git a/docs/af1/af1.3.ipynb b/docs/af1/af1.3.ipynb index a8132b6..9950882 100644 --- a/docs/af1/af1.3.ipynb +++ b/docs/af1/af1.3.ipynb @@ -53,7 +53,7 @@ "source": [ "## Whole-genome sequencing and variant calling\n", "\n", - "All samples in `Af1.3` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " + "All samples in `Af1.3` have been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " ] }, { @@ -648,9 +648,9 @@ }, "environment": { "kernel": "mgenv_7.2.0", - "name": "workbench-notebooks.m138", + "name": "workbench-notebooks.m139", "type": "gcloud", - "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139" }, "kernelspec": { "display_name": "Python (mgenv_7.2.0)", diff --git a/docs/af1/af1.4.ipynb b/docs/af1/af1.4.ipynb index 6d26352..854cb79 100644 --- a/docs/af1/af1.4.ipynb +++ b/docs/af1/af1.4.ipynb @@ -57,7 +57,7 @@ "source": [ "## Whole-genome sequencing and variant calling\n", "\n", - "All samples in `Af1.4` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " + "All samples in `Af1.4` (except for the samples in 1354-VO-KE-DONNELLY-VMF00281) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1354-VO-KE-DONNELLY-VMF00281 have been sequenced individually to high coverage by BMKGENE. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " ] }, { @@ -685,9 +685,9 @@ }, "environment": { "kernel": "mgenv_7.2.0", - "name": "workbench-notebooks.m138", + "name": "workbench-notebooks.m139", "type": "gcloud", - "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139" }, "kernelspec": { "display_name": "Python (mgenv_7.2.0)", From 8e1373a40080df63671baa812b1ad10bd8a1561b Mon Sep 17 00:00:00 2001 From: jonbrenas Date: Sun, 15 Mar 2026 19:23:22 +0000 Subject: [PATCH 2/2] Corrected typo --- docs/af1/af1.1.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/af1/af1.1.ipynb b/docs/af1/af1.1.ipynb index 05eb4ab..c95b7db 100644 --- a/docs/af1/af1.1.ipynb +++ b/docs/af1/af1.1.ipynb @@ -68,7 +68,7 @@ "source": [ "## Whole-genome sequencing and variant calling\n", "\n", - "All samples in `Af1.1` (except for the samples in 1236-VO-TZ-OKUMU-VMF00248 and the samples in small-2020-af) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00248 ahve been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " + "All samples in `Af1.1` (except for the samples in 1236-VO-TZ-OKUMU-VMF00248 and the samples in small-2020-af) have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. All samples in 1236-VO-TZ-OKUMU-VMF00248 have been sequenced individually to high coverage by Novogene. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. " ] }, {