Alisa Vershinina, PhD

Alisa Vershinina, PhD

Scientist (mostly) | artist (sometimes) | 'omics person

Blog posts

2019

2018

Creating consensus fasta using iupac codes

less than 1 minute read

Published:

Fasta files can be generated from vcf calls. There are two ways of doing that: (1) concatenate snips together (this can be done using either variants only or calling monomarphic (hom ref) variants as well and concatenating them too); (2) use reference genome as a backbone and incorporate variants into the reference. To incorporate information about heterozygotes, IUPAC substitution codes can be used. Here is a collection of scripts available:

Tools to deal with aDNA damage

less than 1 minute read

Published:

  • mapDamage –rescale option changes quality scores on bam files
  • PMDtools - filters out contaminant reads based on deamination profiles AND adjust scores too. Works on SAM files.
  • ATLAS toolset can do BQSR
  • AntCaller - genotype caller for ancient genomes. Works better than GATK according to the paper.
  • SpAl - estimate the proportion of spurious alignments in ancient DNA. Works with any species, as long as there is data on variation in the genome.

2016

Should we BQSR ancient genomes?

1 minute read

Published:

A regular protocol for variant discovery pipeline includes base call recalibration after an alignment to a reference genome. This is usually done by GATK. Recalibration accounts for the fact that quality scores sometimes can depend on a cluster density of the sequencing machine, length of the read, position of a bp in the read and other factors. When sequencing ancient DNA, all these parameters go out the window because of DNA post mortem damage (PMD). So should we recalibrate anyway?

Note on f3 statistic calculation

2 minute read

Published:

f3 statistic was developed by Patterson and Reich to measure admixture between populations. It is widely used in ancient DNA studies and there are many packages out there which are able to estimate it for you.