extend pipeline for genotype calling and genotype likelihood - Githubissues

rvosa / arangs2016

Automated and Reproducible Analysis of Next Generation Sequencing data (ARANGS16)

http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS16

MIT License

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extend pipeline for genotype calling and genotype likelihood #12

Open sjordi opened 8 years ago

sjordi commented 8 years ago

install GATK in a docker containe. GATK github repository
call genotypes using gatk
install ANGSD in a docker container
calculate genotype likelihood with ANGSD
extend pipeline script to include genotype calling and genotype likelihood
run pipeline
compare results between threshold genotype calling and genotype likelihood
push GATK and ANGSD containers to Docker hub for later re-usage