Data from Repeated Plague Infections Across Six Generations of Neolithic Farmers

# Public data from 'Repeated Plague Infections Across Six Generations of Neolithic Farmers'

This archive contains human (hg19) and Yersinia pestis bam alignment files and genotype data from Seersholm et al. 'Repeated Plague Infections Across Six Generations of Neolithic Farmers'

Please note that, with the exception of the Yersinia pestis genotypes, this data is unfiltered and will require some filtering before formal analysis.

## Alignment files mapped to the human hg19 genome
These files follow the naming format: {sampleId}.humanHg19.bam. Please note that these alignment files are unfiltered. We recommend filtering the alignments to remove low quality alignments and duplicate reads as follows:
samtools view -bh -F 0x400 -q30 {sampleId}.humanHg19.bam > {sampleId}.humanHg19.filter.bam

## Alignment files mapped to the Yersinia pestis genome (GCF_000009065.1)
These files follow the naming format: {sampleId}.yPestis.bam. Please note that these alignment files are unfiltered. We recommend filtering the alignments to remove low quality alignments and duplicate reads as follows:
samtools view -bh -F 0x400 -q30 {sampleId}.yPestis.bam > {sampleId}.yPestis.filter.bam

## Imputed genotypes of all 120 individuals from this study
The file 'falbygdenPlague.humanHg19.vcf.gz' contains imputed genotypes from 43,983,251 positions of the human hg19 genome. Please note that this genotype file includes very low coverage individuals and low quality SNP calls which should be removed. We recommend removing all individuals with coverage <0.1X. Furthermore, we recommend applying the following filters: INFO score >= 0.8, MAF >= 0.01.

## Yersinia pestis genotypes for 453 ancient and modern genomes
The file 'falbygdenPlague.yPestis.masked.vcf.gz' contains genotypes of the four high coverage genomes from this study (FRA005, FRA020, FRA013, and FRA102), together with 87 other high coverage ancient genomes, 361 modern genomes and a Yersinia pseudotuberculosis outgroup. Only variant sites contained within the mapability mask used in this study are included.