dmill903/compound-het-vip repository overview

This image contains all the tools needed to identify compound heterozygous variants using VCF or gVCF files (https://github.com/dmiller903/CompoundHetVIP⁠). Tools available and used in the container include: Plink2 (1, 2), Picard (3), GATK4 (4), SAMtools (5), BCFtools (5), SHAPEIT2 (6), Beagle (7), Eagle2 (8), vt (9), SnpEff (10), GEMINI (11), Gene Damage Index (12), vcf2db (13), and any necessary dependencies.

REFERENCES

1. S. Purcell, C. Chang, PLINK 2.0 (www.cog-genomics.org/plink/2.0/⁠).
2. C. C. Chang, C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell, J. J. Lee, Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 4, 7 (2015).
3. Picard Tools, (available at http://broadinstitute.github.io/picard/⁠).
4. R. Poplin, V. Ruano-Rubio, M. A. DePristo, T. J. Fennell, M. O. Carneiro, G. A. Van der Auwera, D. E. Kling, L. D. Gauthier, A. Levy-Moonshine, D. Roazen, K. Shakir, J. Thibault, S. Chandran, C. Whelan, M. Lek, S. Gabriel, M. J. Daly, B. Neale, D. G. MacArthur, E. Banks, Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv (2017), p. 201178.
5. H. Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 27, 2987–2993 (2011).
6. O. Delaneau, B. Howie, A. J. Cox, J.-F. Zagury, J. Marchini, Haplotype estimation using sequencing reads. Am. J. Hum. Genet. 93, 687–696 (2013).
7. S. R. Browning, B. L. Browning, Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).
8. P.-R. Loh, P. Danecek, P. F. Palamara, C. Fuchsberger, Y. A Reshef, H. K Finucane, S. Schoenherr, L. Forer, S. McCarthy, G. R. Abecasis, R. Durbin, A. L Price, Reference-based phasing using the Haplotype Reference Consortium panel. Nat. Genet. 48, 1443–1448 (2016).
9. A. Tan, G. R. Abecasis, H. M. Kang, Unified representation of genetic variants. Bioinformatics. 31, 2202–2204 (2015).

10. P. Cingolani, A. Platts, L. L. Wang, M. Coon, T. Nguyen, L. Wang, S. J. Land, X. Lu, D. M. Ruden, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly . 6, 80–92 (2012).
    

    Copy

11. U. Paila, B. A. Chapman, R. Kirchner, A. R. Quinlan, GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput. Biol. 9, e1003153 (2013).
    

    Copy

12. Y. Itan, L. Shang, B. Boisson, E. Patin, A. Bolze, M. Moncada-Vélez, E. Scott, M. J. Ciancanelli, F. G. Lafaille, J. G. Markle, R. Martinez-Barricarte, S. J. de Jong, X.-F. Kong, P. Nitschke, A. Belkadi, J. Bustamante, A. Puel, S. Boisson-Dupuis, P. D. Stenson, J. G. Gleeson, D. N. Cooper, L. Quintana-Murci, J.-M. Claverie, S.-Y. Zhang, L. Abel, J.-L. Casanova, The human gene damage index as a gene-level approach to prioritizing exome variants. Proc. Natl. Acad. Sci. U. S. A. 112, 13615–13620 (2015).
    

    Copy
13. https://github.com/quinlan-lab/vcf2db⁠