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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:
- 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.
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?
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.
There are several potential problems if you call SNPs from low coverage ancient samples:
Undergraduate course, UCSC EEB, 2018
We were at the end of the Earth
Assignment, UCSC EEB, 2018
Opening the command line
Tutorial, UCSC EEB, 2019
What am I loking for? What is the purpose of my search? What are the keywords?
Mentorship, UCSC EEB, 2019
Were you my mentee??? Your feedback is very important for me. I would be grateful if you could answer the following questions. Answering them is up to you, feel free to leave any questions (or all of them) unanswered. Your answers may vary depending on whether you were an undergraduate or graduate student, so mark with NA points that are not applicable to your experience.