From 2dbebb4d97e15d0d5fcf303a4466314b1f313208 Mon Sep 17 00:00:00 2001 From: sidharthgoel Date: Sun, 6 Dec 2020 17:10:36 -0800 Subject: [PATCH] Minor updates to DeepTrio Pacbio case study. PiperOrigin-RevId: 345994033 --- docs/deeptrio-pacbio-case-study.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/deeptrio-pacbio-case-study.md b/docs/deeptrio-pacbio-case-study.md index 33703ebf..19e1c4da 100644 --- a/docs/deeptrio-pacbio-case-study.md +++ b/docs/deeptrio-pacbio-case-study.md @@ -1,8 +1,9 @@ # Using DeepTrio for small variant calling from the trio sequenced with PacBio HiFi -In this case study, we describe applying DeepTrio to a real WGS trio. Then we -assess the quality of the DeepTrio variant calls with `hap.py`. In addition we -evaluate a mendelian violation rate for a merged VCF. +In this case study, we describe applying [DeepTrio](deeptrio-details.md) to a +real PacBio WGS trio. Then we assess the quality of the DeepTrio variant calls +with `hap.py`. In addition we evaluate a Mendelian violation rate for a merged +VCF. To make it faster to run over this case study, we run only on chromosome 20. @@ -84,15 +85,17 @@ is run as a separate command. mkdir -p output mkdir -p output/intermediate_results_dir -BIN_VERSION=1.0.1rc +BIN_VERSION="1.1.0" -sudo docker pull gcr.io/deepvariant-docker/deeptrio:"${BIN_VERSION}" +sudo apt -y update +sudo apt-get -y install docker.io +sudo docker pull google/deepvariant:deeptrio-"${BIN_VERSION}" time sudo docker run \ -v "${PWD}/input":"/input" \ -v "${PWD}/output":"/output" \ -v "${PWD}/reference":"/reference" \ - gcr.io/deepvariant-docker/deeptrio:"${BIN_VERSION}" \ + google/deepvariant:deeptrio-"${BIN_VERSION}" \ /opt/deepvariant/bin/deeptrio/run_deeptrio \ --model_type PACBIO \ --ref /reference/GRCh38_no_alt_analysis_set.fasta \