Python functions and jupyter notebooks used in QTL analysis of Cryptococcus neoformans hypermutator phenotype in Priest et al. 2021
- Used for analysis and visualization
- Used to align FASTQ file to an XL280 reference genome
- Used to generate and filter SAM and BAM files
Freebayes v 1.2.0 haplotype caller
- Used to detect genetic variants segregating in the mapping population
- Used to add read group information to BAM
- A notebook that constructs bash calls for aligning paired-end reads with BWA, SAM to BAM conversion, adding readgroups, and calling freebayes for variant detection
- A library of dataframes, lists, variables, and functions used across notebooks.
- Transforms and addjusts labels and scles of hypermutator phenotype data.
- Filters the variant call files across chromosomes and generates supplementary Figure S14 in Priest et al.
- Reformats genotpe data and sample names for use in QTL mapping.
- Merges chromosome variant data and data from the reference genome to construct a map associated chromosome names and numbers (as well as other data).
- Plots the haplotypes across chromosome 3 and 11, generating supplementary Figure S5 in Priest et al.
- For the QTL regions on chromosome 3 and 11, predicts the changes in amino acid sequnces for genes within these QTL.
- Codnducts QTL analysis of hyptermutator phenotype and genotypes in Bt65 x H99 F1 progeny, generating upper panel of Figure 2 and Supplementary Figure S4 as seen in Priest et al.
- For each sampled progeny sequenced from the Bt65 x H99 cross, constructs diagnostic plots of allele, read-depth, allelic read-depth across chromosomes. The plot for progney P25 was used as Supplementary Figure S13 in Priest et al.
- Plots the gene model, variants, and amino acids for CNAG_02700 used in middle panel of Figure 2 in Priest et al.
- Plots the gene model, variants, and amino acids for CNAG_01836 used in upper panel of Supplementary Figure S7 in Priest et al.