J2-M172 phylogeny research

See gdriv.es/J2-M172/J2a-M410/ (Google Drive Folder)

Y-sequence evidence data for variant and haplogroup research

  1. sample read/alignment raw data (.BAM files): 1000 Genomes, BigY, FGC Y-Elite
  2. sample variants and coverage data (.VCF + .BED, CGI/CGA): BigY, PGP, EstonianBiocentre?
  3. sample known variants status and novel variant data lists (.CSV, etc.): BigY, FGC
  4. shared and sample variant data lists (.CSV, etc.): Francalacci, Hallast
  5. shared variant data lists (.CSV, etc.): GoNL
  6. sample known variants status (.CSV, etc.): Geno 2.0, Chromo2

1. is able to certify SNP positions for ISOGG (enough read quality given). 2. can give a very confident prediction of SNP positions but no final certification (quality settings might “hide” some informative reads). 3.-4. have the potential to build a confident phylogeny, but need certification 5.-6. are usually able to confirm well known (or otherwise covered) branches, but have limited value for novel terminal branch research and certification.