Public | Automated Build

Last pushed: 4 months ago
Short Description
Docker for iAdmix to calculate population allele frequency for the input .vcf file.
Full Description

dockerhub-iadmix

Docker container for iadmix

build a docker container from the latest Dockerfile in Git Hub

docker build -t j5kim/iadmix:latest github.com/jihoonkim/dockerhub-iadmix

push the built Docker image to Docker Hub

docker login
docker push j5kim/iadmix:latest

test run docker with an example input

docker run -t -i j5kim/iadmix:latest /bin/bash /testrun/testrun.sh

How to create the example .vcf file for a test run (individual NA12878)

wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.1/GRCh37/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.1_highconf_phased.vcf.gz

gunzip HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.1_highconf_phased.vcf.gz

mv HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.1_highconf_phased.vcf HG001.vcf

vcftools --vcf HG001.vcf --chr 22 --recode --out /testrun/HG001_chr22.vcf

Test run is success if the last line of final ouput, /testrun/HG001_chr22.vcf.INTEGRATION.input.ancestry, has the following allele frequencies

MKK:0.1887 CEU:0.8113 FINAL_NZ_PROPS

run with a user's own input .vcf data

docker run -t -i -m 4g -v /Users/JohnDoe/mylocaldirectory:/mydata j5kim/iadmix:latest /bin/bash /workflow/workflow.sh /mydata/my.vcf

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j5kim
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