HaploTypo: a variant-calling pipeline for phased genomes
HaploTypo: a variant-calling pipeline for phased genomes
Citació
- Pegueroles C, Mixão V, Carreté L, Molina M, Gabaldón T. HaploTypo: a variant-calling pipeline for phased genomes. Bioinformatics. 2020; 36(8):2569-71. DOI: 10.1093/bioinformatics/btz933
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Descripció
Resum
SUMMARY: An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. AVAILABILITY AND IMPLEMENTATION: HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.