Variant Discovery and Genome Assembly
Melissa Wilson Sayres
Sex Differences in Reference Genome Affect Variant Calling and Differential Expression
X and Y homology dotplot
- a few regions of alignment (PAR)
@sexchrlab
doi.org/10.1101/346940
- https://www.biorxiv.org/content/early/2018/07/18/346940
- preprint on correct tech biases on sex chr in NGS data
- infer sex chromosome complement
- pointing out regions on autosomes with sex chr - like alignment
- which is screwing up read balance
- which presumably could influence variant calling
chrY var calls will have many errors
- 10,000 variants can be missed
- mostly in PAR
Prithika Sritharan (Dicks)
Encoding yeast genomic diversity using variation graphs
Yeast
“one of earliest species to be domesticated”
NCYC
- 4,000 strains of 530 species of yeast
- 1,000 have been sequenced
Want to characterize these
Want to avoid conventional ref genome
- doesn’t represesent all species well
Variation Graphs
- using VG Toolkit (Garrison et al. 2017)
- can align way more to VG than a traditional linear reference
- looks WAY more, but y axis kind of deceiving (87-99% scale)
Zemin Ning (Durbin)
ScaffHiC Genome Scaffolding by Modelling Distributions of Hi-C Paired-end Reads
Contact matrix
- C(i,j) num of paired reads between i and j contigs
- curve fit contact distance with (rougly) quadratic model
- also use orientation of reads
Quantify contig distance index
difficult to pick ‘favorite’ contig partner
showing stats of icefish genome assmembly which has better n50 etc stats than other tools