VCF, pileup, and other files for Betula analyses using ebg & GATK

These are the VCF, pileup, and input files files produced by the Genome Analysis ToolKit, SAMtools, and our own scripts, respectively, used for comparing the genotypes estimated by the GATK UnifiedGenotyper and the new model for allopolyploids that we introduced in our paper. Additional processing of the files was conducting using Python and R for filtering and extracting error values and read counts (scripts available on GitHub: https://github.com/pblischak/polyploid-genotyping).

Main files:

• pendula-ug-filtered30.vcf: VCF file from GATK with all called variants for Betula pendula (diploid).
• filtered30-pendula.pileup: SAMtools pileup file for variant sites identified by GATK in B. pendula.
• pubescens-ug-filtered30.vcf: VCF file from GATK with all called variants for Betula pubescens (allotetraploid).
• filtered30-pubescens.pileup: SAMtools pileup file for variant sites identified by GATK in B. pubescens.

Processed files:

• filtered30-variants.txt: tab delimited file of shared variants between B. pendula and B. pubescens.
• filtered30-vcf1.vcf: VCF file for B. pendula with variants extracted from filtered30-variants.txt.
• filtered30-vcf2.vcf: VCF file for B. pubescens with variants extracted from filtered30-variants.txt.

Input files:

• filtered30-pubescens-tot.txt, filtered30-pubescents-alt.txt, filtered30-pubescens-err.txt: input files for running the alloSNP model in ebg.
• filtered30-pubescens-alloSNP-freqs2.txt, filtered30-pubescens-alloSNP-g1.txt, filtered30-pubescens-alloSNP-g2.txt: output files from the alloSNP model.
• filtered30-pendula-tot.txt, filtered30-pendula-alt.txt, filtered30-pendula-err.txt: input files for running the hwe model in ebg.
• filtered30-pendula-hwe-freqs.txt, filtered30-pendula-hwe-genos.txt: output files from the hwe model. The allele frequency estimates here were also used as the reference panel for the alloSNP model.