diff --git a/README.md b/README.md index 0f3658d5..a4ea10e2 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,4 @@ ![Imputationserver Logo](logo.png) -[![Publication](https://img.shields.io/badge/Published-Nature%20Genetics-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/ng.3656) -[![Build Status](https://travis-ci.org/genepi/imputationserver.svg?branch=master)](https://travis-ci.org/genepi/imputationserver) -[![codecov](https://codecov.io/gh/genepi/imputationserver/branch/master/graph/badge.svg)](https://codecov.io/gh/genepi/imputationserver) - follow on Twitter -This repository includes the complete source code for the [Michigan Imputation Server](https://imputationserver.sph.umich.edu) workflow based on Minimac4. -The workflow itself is executed with the [Cloudgene workflow system](https://github.com/genepi/cloudgene) for Hadoop MapReduce. - -Michigan Imputation Server consists of several parallelized pipeline steps: - -- Quality Control -- QC Report -- Phasing and Imputation -- Compression and Encryption - -## Documentation -The documentation is available at http://imputationserver.readthedocs.io. - -## Citation -Please cite this paper if you use Michigan Imputation Server: - -> Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze S, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C. [Next-generation genotype imputation service and methods](https://www.ncbi.nlm.nih.gov/pubmed/27571263). Nature Genetics 48, 1284–1287 (2016). - -## Contact - -Feel free to contact [us](https://imputationserver.sph.umich.edu/index.html#!pages/contact) in case of any problems. - -## Contributors - -- Lukas Forer -- Sebastian Schönherr -- Sayantan Das -- Christian Fuchsberger - -## Contributing -Project contributions are more than welcome! See our [CONTRIBUTING.md](CONTRIBUTING.md) file for details. +This repository is a fork of https://github.com/genepi/imputationserver diff --git a/files/minimac4.yaml b/files/minimac4.yaml index ba92c8a2..8e3876c2 100644 --- a/files/minimac4.yaml +++ b/files/minimac4.yaml @@ -1,7 +1,7 @@ id: imputationserver name: Genotype Imputation (Minimac4) description: This is the new Michigan Imputation Server Pipeline using Minimac4. Documentation can be found here.

If your input data is GRCh37/hg19 please ensure chromosomes are encoded without prefix (e.g. 20).
If your input data is GRCh38hg38 please ensure chromosomes are encoded with prefix 'chr' (e.g. chr20). -version: 1.5.8 +version: 1.5.8-genotek website: https://imputationserver.readthedocs.io category: diff --git a/pom.xml b/pom.xml index 30136ffb..628dab93 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ genepi imputationserver - 1.5.8 + 1.5.8-genotek jar University of Michigan Imputation Server diff --git a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java index e43b6a89..99bf4600 100644 --- a/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java +++ b/src/main/java/genepi/imputationserver/steps/imputation/ImputationPipeline.java @@ -23,7 +23,7 @@ public class ImputationPipeline { - public static final String PIPELINE_VERSION = "michigan-imputationserver-1.5.8"; + public static final String PIPELINE_VERSION = "michigan-imputationserver-1.5.8-genotek"; public static final String IMPUTATION_VERSION = "minimac4-1.0.2"; diff --git a/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java b/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java index 01852193..1171b9ff 100644 --- a/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java +++ b/src/main/java/genepi/imputationserver/util/DefaultPreferenceStore.java @@ -71,13 +71,15 @@ public static Properties defaults() { defaults.setProperty("chunksize", "20000000"); defaults.setProperty("phasing.window", "5000000"); defaults.setProperty("minimac.window", "500000"); + defaults.setProperty("minimac.vcores", "1"); + defaults.setProperty("eagle.vcores", "1"); defaults.setProperty("minimac.sendmail", "no"); defaults.setProperty("server.url", "https://imputationserver.sph.umich.edu"); defaults.setProperty("minimac.tmp", "/tmp"); defaults.setProperty("minimac.command", "--refHaps ${ref} --haps ${vcf} --start ${start} --end ${end} --window ${window} --prefix ${prefix} --chr ${chr} --cpus 1 --noPhoneHome --format GT,DS,GP --allTypedSites --meta --minRatio 0.00001 ${chr =='MT' ? '--myChromosome ' + chr : ''} ${unphased ? '--unphasedOutput' : ''} ${mapMinimac != null ? '--referenceEstimates --map ' + mapMinimac : ''}"); defaults.setProperty("eagle.command", - "--vcfRef ${ref} --vcfTarget ${vcf} --geneticMapFile ${map} --outPrefix ${prefix} --bpStart ${start} --bpEnd ${end} --allowRefAltSwap --vcfOutFormat z --keepMissingPloidyX"); + "--numThreads ${eagle.vcores} --vcfRef ${ref} --vcfTarget ${vcf} --geneticMapFile ${map} --outPrefix ${prefix} --bpStart ${start} --bpEnd ${end} --allowRefAltSwap --vcfOutFormat z --keepMissingPloidyX"); defaults.setProperty("beagle.command", "-jar ${beagle} ref=${ref} gt=${vcf} out=${prefix} nthreads=1 chrom=${chr}:${start}-${end} map=${map} impute=false"); defaults.setProperty("ref.fasta", "v37");