Epigenomics genotyping pipeline

Nextflow pipeline for genotyping from epigenomics data

Requirements

• Nextflow (https://www.nextflow.io/)
• samtools (http://www.htslib.org/)
• bcftools (http://www.htslib.org/)
• pyfaidx (https://github.com/mdshw5/pyfaidx)

Pipeline overview

Samples BAM files are merged by corresponding individual and then used for a bcftools-based genotyping pipeline. Genetic relatedness calculated using plink2.

Usage

[sabramov@dev0 ~]$ nextflow run genotyping.nf -profile Altius
[sabramov@dev0 ~]$ nextflow run clustering.nf -profile Altius

Input

Sample file [--samples_file]

A tab-delimited file containing information about each sample. The file must contain a header and the following columns (other columns are permitted and ignored):

• indiv_id: Individual identifier for each sample; many samples can refer to one individual
• bam_file: Absolute path the BAM-formated file

Genome reference [--genome_fasta_file]

dbSNP reference [--dbsnp_file]

Ancestral genome [--genome_ancestral_fasta_file]

Encode blacklisted regions [--encode_blacklist_regions]

Additonal Parameters:

Chunk size [--chunksize 5000000]

Specificies the size (in base-pairs) to use when dividing the genome into chunks for parallel processing.

SNP quality [--min_SNPQ 10]

Filter variants with poor quality

Genotype quality [--min_GQ 50]

Set genotype for an individual to ./. (missing) when genotyping score (FORMAT/GQ) is less than this value.

Sequencing depth [--min_DP 12]

Minimum sequencing depth per individual to call heterozygous sites.

Per-allele depth [--min_AD 4]

Minimum sequencing depth at each allele per individual to call heterozygous sites.

Hardy-Weinberg equilbrium [--hwe_cutoff 0.01]

Filter variants that are out of Hardy-Weinberg equilibrium (p-value threshold)

Output directory [--outdir output]

Specify output direectory

Output

The pipeline outputs a single VCF-formated file containing the called and filtered genotypes for each distinct invididual in the samples file. Each variant is annotated with the following extra infornation:

• ID field: dbSNP rs number
• INFO/CAF: 1000 genomes project allele frequency (from dbSNP annotation file)
• INFO/TOPMED: TOPMED project allele frequency (from dbSNP annotation file)
• INFO/AA: Inferred ancenstral allele from EPO/PECAN alignments (see "Input" for information about how this is obtained)