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Y-DNA tools

From ISOGG Wiki

There are a number of Y-DNA tools that can be used to analyse Y-chromosome DNA results including predicton of haplogroups.

Note that this list is provided for information only. Inclusion on this list does not imply recommendation or endorsement by ISOGG.

Y-STR haplotype tools (modals, genetic distance, TMRCA)

The following is a selection of tools that can be used for a set of Y-STR values (DYS etc.) including calculating the time to the most recent common ancestor.

Y-STR haplogroup prediction tools

The accuracy of haplogroup prediction based on Y-STR haplotypes depends mainly on the number of STR values. Without SNP confirmation prediction for low-resolution haplotypes (Y-STR12 to Y-STR25) has a low value of confidence and convergence can be a problem. For many haplogroups Y-STR25 to Y-STR37 has an acceptable confidence level while for some young haplogroups with rapid diversification and expansion like in R1b even Y-STR111 is not enough to discriminate the correct sub-lineage with confidence. A few scientific studies are available.[1] [2] [3] However, with the growth of next generation sequencing tests and whole genome sequencing which report on both STRs and SNPs in a single test, the use of STR-based tests and the need for haplogroup prediction tools is in decline.

Y-SNP haplogroup prediction tools

YBrowse - The ISOGG human Y-chromosome browser

Maintained by Thomas Krahn of YSEQ, ISOGG YBrowse is a free resource for detailed data about Y chromosome STRs and SNPs. Currently using reference assembly hg38, users can enter the name of an individual SNP, STR, or a loci range and the interactive display will show elements such as a graphic of the relative position on the chromosome, the actual locus number(s), the range covered by an STR (and SNPs encompassed, if any), synonymous SNP names, and SNP ancestral allele. Additionally, YBrowse makes available for download the datasets it is currently using. These are updated frequently and include files in FASTA, GFF (Generic Feature Format), VCF (Variant Call Format), and CSV versions.

Y-STR and Y-SNP databases

   See main article: DNA databases

  • mitoYDNA.org A crowdsourced Y-DNA and mtDNA database, with tools and analysis
  • YHRD.org, World Y-database with over 160,000 haplotypes, 1015 populations, 33 metapopulations, Sascha Willuweit & Lutz Roewer, 2000-2016
  • Yfiler haplotype database

General Y-DNA tools

  • FamilyTreeDNA Discover A free website from FamilyTreeDNA where can learn more about your haplogroup.
  • Ancestral DNA Marker Pedigree Display A tool from Brad Larkin which allows the user to display the SNP progression for a single ancestral line
  • Genetic Homeland DNA Marker Index A free resource from Brad Larkin which provides an index of markers and their RSID positions on all 23 chromosomes.
  • Rob Spencer's SNP Tracker Provides a SNP progression list, timelines and maps based on FTDNA BigY data
  • FT2DNA Dave Hamm's utility to convert Family Tree DNA's Y-chromosome repeat data format into raw code (i.e.: ATGC) for analysis by other utilities such as PHYLIP.
  • FT2PHY Dave Hamm's tool for the conversion of FTDNA repeat data format files into ATGC format files for use with PHYLIP compatible packages, such as DNAML. This program uses input that is compatible with Dean McGee's Y-DNA Utility, but is limited to 37 markers.
  • Ann Turner's Mutation Calculator A tool to calculate Y DNA mutations.
  • YGED Roger Arrick's program simplifies the creation of GEDCOM files for the Y-DNA line
  • Y Heatmap A Y-chromosome mapping tool developed by Hunter Provyn in cooperation with YSEQ and YFull
  • Time to most-recent common ancestor (TMRCA) estimates for targetted pairs A tool provided by Iain Macdonald which will perform comparisons based on Y-chromosome sequencing tests and 111 Y-STR tests.

Next generation sequencing tools

  • YFull A raw data (BAM) interpretation and analysis service (online) for full Y-chromosome data
  • Full Genomes Corporation Offers also a BAM file analysis service (Big Y etc.)
  • clarifY DNA A Big Y analysis service providing personalised reports and diagrams showing placement on the phylogenetic tree. See the review by Debbie Kennett clarifY DNA - a new Y-SNP analysis service
  • Brad Larkin's NextGenMatch tool. The tool is available on Brad's Genetic Homeland website. The tool is free to use but registration is required. For details see Brad's post on the GenealogyDNA mailing list
  • Felix Immanuel's Big Y BAM analysis tool
  • Integrative Genomics Viewer (IGV) A tool provided the Broad Institute which allows the user to analyse BAM files, needs registration with email
  • Galaxy Open source, web-based platform for data intensive NGS research, included are SAMtools, BamTools, Picard, VCF Manipulation, etc., User account suggested
  • SNPdata A free tool for comparing build 37/19 and build 38 Y-chromosome data. it contains a search for dual SNP positions
  • WGS Extract A locally-installed desktop combined utility that allows extraction of information from common 30X coverage whole genome sequencing results. Three options are available for Y-DNA processing: 1) Generate a Y- and Mitochondrial-only BAM (for use at YFull); 2) Generate a Y-only BAM (for use at Y-DNA Warehouse or other sites that only need a Y BAM); 3) Generate an annotated Y VCF file for use at YFull in lieu of a BAM, or with Clade Finder or similar. It can be used on BAM/CRAM files from common testing providers like Dante Labs, Nebula Genomics, YSEQ, Full Genomes Corporation, and others.
  • BAMsAway A Chrome extension for analysis of BigY BAM files. If you enter the Y-DNA position, the extension will show you the actual reads at that position.

Y-Sequence Trees (TMRCA, ancient Y)


Further reading

Scientific papers

See also

References

  1. ↑ Wang et al 2013 (preprint): Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction, http://arxiv.org/abs/1310.5413
  2. ↑ Larmuseau et al 2014: Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance, http://dx.doi.org/10.1111/ahg.12050
  3. ↑ Woźniak et al 2006: Correlations between haplogroup membership and Y-STR haplotype as a potential measure of quality control in forensic examinations [in Polish], http://www.ncbi.nlm.nih.gov/pubmed/17131759
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