Description
The Modern Human Variants track shows variant calls made from sequence
reads of eleven individuals mapped to the human genome. The purpose of
this track is to put the divergence of the Denisova genome into
perspective with regard to present-day humans.
Methods
DNA was obtained for each of ten individuals from the
CEPH-Human Genome Diversity Panel (HGDP):
- HGDP00456 (Mbuti)
- HGDP00521 (French)
- HGDP00542 (Papuan)
- HGDP00665 (Sardinian)
- HGDP00778 (Han)
- HGDP00927 (Yoruba)
- HGDP00998 (Karitiana)
- HGDP01029 (San)
- HGDP01284 (Mandenka)
- HGDP01307 (Dai)
DNA was also extracted from a Dinka individual from Sudan (DNK02).
To minimize biases due to instrument variability, the samples were pooled
for sequencing, using four barcoded libraries per sample.
The paired-end reads were aligned to the human genome
using the Burrows-Wheeler Aligner and potential PCR duplicates
were filtered using
Picard.
Genotype calls for single nucleotide variants and small insertions and
deletions were made using the Unified Genotyper from the
Genome Analysis Toolkit (GATK), with an additional iteration
using a modified reference genome in order to reduce reference bias
(Note 6,
supplementary online materials of Meyer, 2012).
Variant Call Format (VCF) files were enhanced by adding information from
Ensembl Compara EPO alignments of 6 primates and of 35 Eutherian mammals,
phastCons conservation scores generated using EPO alignments,
1000 Genomes Project
integrated variant call files,
University of Washington
background selection scores,
ENCODE/Duke Uniqueness of 20mers (see the Mappability track),
segmental duplications from the Eichler lab (see the Segmental Dups track),
and
samtools mpileup summaries of mapped reads.
Credits
Thanks to the
Max Planck Institute for Evolutionary Anthropology
for providing the variant-only VCF files used for this track.
References
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de
Filippo C et al.
A high-coverage genome sequence from an archaic Denisovan individual.
Science. 2012 Oct 12;338(6104):222-6.
PMID: 22936568; PMC: PMC3617501;
supplementary online materials, Note 6.
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