honeybee genotype pipeline

Preconfigured pipeline for converting Illumina reads into VCF for Apis mellifera. The input should be demultiplexed. Reads for each sample should be non-interleaved (i.e. separate r1 and r2 files).

1. Check pairing
2. Strict barcode check
3. Filter contaminants
4. Trim adaptors
5. Map against reference genome
6. Call SNPs with freebayes (each contig run separately in parallel)
7. Genotyping stats

In another pipeline (coming soon):

• Make a set of haplotypes from the haploid individuals (drones)
• Use whatshap to set this as a haplotype and phase the pools

Install

Use the singularity container from the Releases tab or the Docker container from GHCR. The container provides:

bbmap 38.90
bwa 0.7.17-r1188
freebayes 1.3.2
python 3.8.5
R 3.6.3 with data.table 1.12.8 and ggplot2 3.3.0
samtools 1.10 and bcftools 1.10.2 using htslib 1.10.2-3
vcflib 1.0.1
vcftools 0.1.16

If you have the above dependencies installed, you can install the pipeline with pip3:

pip3 install \
    git+git://github.com/tomharrop/honeybee-genotype-pipeline.git

Usage

• threads: Number of threads to use. Intermediate files are pipes, so at least 4 threads are required.
• restart_times: Number of times to restart failing jobs.
• ref: Reference genome (uncompressed fasta).
• samples_csv: a csv file with the following columns:
  • sample: sample name (will be propagated to output files and VCF);
  • barcode: sample barcode, will be checked with 0 allowed mismatches;
  • r1_path: path to R1 file for this sample;
  • r2_path: path to R2 file for this sample;
  • metadata (optional): currently not used.
• outdir: Output directory.
• cnv_map: Read in a whitespace-delimited file of sample names and ploidy, e.g. for genotyping drones and pools in a single run. See freebayes --help for more info.
• ploidy: Ploidy for freebayes, e.g. 1 for haploid, 2 for diploid.
• csd: Do a separate freebayes run to pick up all alleles at the csd locus (i.e. --region NC_037640.1:11771679-11781139).

honeybee-genotype-pipeline [-h] [-n] [--threads int]
                                  [--restart_times RESTART_TIMES] --ref REF
                                  --samples_csv SAMPLES_CSV --outdir OUTDIR
                                  [--cnv_map CNV_MAP | --ploidy PLOIDY]
                                  [--csd]

optional arguments:
  -h, --help            show this help message and exit
  -n                    Dry run
  --threads int         Number of threads. Default: 4
  --restart_times RESTART_TIMES
                        number of times to restart failing jobs (default 0)
  --ref REF             Reference genome in uncompressed fasta
  --samples_csv SAMPLES_CSV
                        Sample csv (see README)
  --outdir OUTDIR       Output directory
  --cnv_map CNV_MAP     Read a copy number map from the BED file FILE
  --ploidy PLOIDY       Ploidy for freebayes (e.g. 1 for haploid, 2 for
                        diploid)
  --csd                 Do a separate freebayes run to genotype the csd locus

Graph

n.b. freebayes doesn't print in the snakemake rulegraph, because it comes after a checkpoint rule. The input is from markdup and generate_regions.