Open Access Highly Accessed Methodology article

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Anneleen Van Geystelen12, Ronny Decorte13 and Maarten HD Larmuseau134*

Author Affiliations

1 UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium

2 Department of Biology, KU Leuven, Laboratory of Entomology, Leuven, Belgium

3 Department of Imaging & Pathology, KU Leuven, Forensic Medicine, Kapucijnenvoer 33, Leuven, B–3000, Belgium

4 Department of Biology, KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium

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BMC Genomics 2013, 14:101  doi:10.1186/1471-2164-14-101

Published: 13 February 2013

Additional files

Additional file 1: Table S1:

The latest version of the Y-SNP conversion file (May 2012). This list contains the name, the synonyms, the RefSNP ID, the position on the Y-chromosome according to references NCBI36 (Hg18) and GRCh37 (Hg 19) and the mutant conversion state (Ancestral allele -> Mutant allele) of all reported Y-SNPs. Table S2. Table-format of the latest full published Y-chromosomal phylogenetic tree of [11]. For each reported Y-chromosomal (sub-)haplogroup, the phylogenetic lineage whereto the (sub-)haplogroup belongs, called the ‘parental lineage’, and the defining Y-SNPs of the lineage are given. Table S3. Table format of the updated Y-chromosomal phylogenetic tree based on the most recent scientific publications (May 2012). For each reported Y-chromosomal (sub-)haplogroup, the phylogenetic lineage whereto the (sub-)haplogroup belongs, called the ‘parental lineage’, and the defining Y-SNPs of the lineage are given. Table S4. Characteristics and AMY-tree results of the test panel with samples from the Complete Genomics (CG), Irish genome (IrG), Khoisan and Bantu Genomes (KBG) and 1000 Genomes (1000G) projects. For each sample the population as well as the ancestral continent of the population is given, next to the relationship with other samples of the test panel. Abbreviations of the populations are ASW: African ancestry in Southwest USA; CEU: Utah residents with Northern & Western European ancestry from the CEPH collection; CHB: Han Chinese in Beijing, China; GIH: Gujarati Indian in Houston, Texas, USA; JPT: Japanese in Tokyo, Japan; LWK: Luhya in Webuye, Kenya; MKK: Maasai in Kinyawa, Kenya; MXL: Mexican ancestry in Los Angeles, California, USA; NK: Khoisan from Northern Kalahari; SA: Bantu from South Africa; SK: Khoisan from Southern Kalahari; TSI: Toscans in Italy; PUR: Puerto Rican in Puerto Rico; YRI: Yoruba in Ibadan, Nigeria. Table S5. Characteristics and AMY-tree results of samples of which the sub-haplogroups was previously reported in literature. Samples are taken from the Complete Genomics (CG), Irish genome (IrG), Khoisan and Bantu Genomes (KBG) and 1000 Genomes (1000G) project. For each sample the population as well as the ancestral continent of the population is given, next to the relationship with other samples of the test panel. Abbreviations of the populations are CEU: Utah residents with Northern & Western European ancestry from the CEPH collection; MXL: Mexican ancestry in Los Angeles, California, USA; NK: Khoisan from Northern Kalahari; SA: Bantu from South Africa; SK: Khoisan from Southern Kalahari; TSI: Toscans in Italy; PUR: Puerto Rican in Puerto Rico; YRI: Yoruba in Ibadan, Nigeria. The sub-haplogroup as it is given in the literature is compared to the determined sub-haplogroups in Karafet and Update tree.

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Additional file 2: Figure S1:

Call quality test scores for 118 samples from different genome sequencing projects created within the AMY-tree algorithm. All samples are ordered according to their project and their number of called Y-SNPs. Figure S2. Relationship between call quality test score and number of Y-SNPs called against hg18 for 118 samples from different genome sequencing projects.

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Additional file 3:

Supplementary Method.

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