config_example1.yaml

 # ---------------- Global parameters ----------------
Ensembl_FTP_URL: ftp.ensembl.org/pub/release-111/
annotationFilename: Homo_sapiens.GRCh38.111.chr_patch_hapl_scaff
ensembl_release: 111

contaminants_fasta: "crap.fasta"      # Path to the FASTA file with contaminant sequences

custom_transcript_list: "data/transcripts_reference_111.csv"
included_transcript_biotypes: ""
only_MANE_select: True

final_fasta_file: "results/example1_concatenated_database.fa"
fasta_simplify_headers: True

# ---------------- ProHap parameters ----------------
use_ProHap: True

phased_FTP_URL: ""
phased_local_path: "sample_data/"
phased_vcf_file_name: "sample_chr{chr}_1kGP_GRCh38_phased.vcf"
sample_metadata_file: "igsr_samples.tsv" 

working_dir_name_haplo: haplotypes_tmp

phased_min_af: 0.01
phased_af_field: AF
haplo_min_freq: 0
haplo_min_count: 0

x_par1_to: 2781479        # End position of the first pseudo-autosomal region (PAR) on the X chromosome
x_par2_from: 155701383    # Start position of the second pseudo-autosomal region on the X chromosome

haplo_require_start: 1
haplo_ignore_UTR: 1
haplo_skip_start_lost: 1
max_cores: 1

haplo_fasta_file: "results/example1_haplotype_translations.fa"
haplo_table_file: "results/example1_haplotypes.tsv"

# ---------------- ProVar parameters ----------------
use_ProVar: False
variant_vcf: {}

working_dir_name_var: variants_tmp

var_require_start: 1

var_fasta_file: ""
var_table_file: ""

add_existing_haplo: False
haplo_added_table: ""
haplo_added_fasta: ""