Alisa Vershinina, PhD

Alisa Vershinina, PhD

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

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.

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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:

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?