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config-orig.yaml
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#
# --- NGS-Pipeline joint variant calling settings ---
#
# NOTE: at some point some configuration will be kept at configs/PANELNAME.yaml
# to allow for multiple panels in a single pipeline
optical_dedup: False
instrument: generic
platform: generic
libprep: generic
min_read_qual: 15
read_length: 100
refseq_file: refs/Pv/PvP01_v2/PvP01_v2.fasta
#knownsites_file: refs/pv-known-variants.bed.gz
knownvariants_dir: refs/Pv/PvP01_v2/known-variants
# perform variant calling on all chromosomes as single workflow
complete_region: PvP01_all_v2
# perform targeted variant calling
targetregion_file: refs/Microhaps_inserts.bed
regions:
- PvP01_01_v2
- PvP01_02_v2
- PvP01_03_v2
- PvP01_04_v2
- PvP01_05_v2
- PvP01_06_v2
- PvP01_07_v2
- PvP01_08_v2
- PvP01_09_v2
- PvP01_10_v2
- PvP01_11_v2
- PvP01_12_v2
- PvP01_13_v2
- PvP01_14_v2
- PvP01_API_v2
- PvP01_MIT_v2
# this is amplicon sequencing, so turn off deduplication
deduplicate: False
# set below to True for new samples (for the purpose of submitting to SRA database)
keep_paired_bam: False
# set below to True for structural variant (SV) analysis such as CNV
keep_final_bam: True
# filter to apply for deduplicated BAM
# read_filters: --remove_FR --remove_RF --remove_FF --remove_RR --remove_trans --remove_unmapped --remove_secondary --remove_supplementary
# for below, we keep FR, RF, FF and RR orientation for future SV analysis
read_filters: --remove_trans --remove_unmapped --remove_secondary --remove_supplementary
reads_trimmer_wf: trimmer_null.smk
reads_mapper_wf: mapper_bwa-mem2.smk
# multistep-variant-caller parameters
prepare_sample_directory_flags: --force
sample_variant_caller_flags: --force --no-config-cascade
joint_variant_caller_flags: --force --no-config-cascade
variant_caller_wf: ssf_varcall_gatk_drag.smk
gatk_calibrate_str: False
haplotypecaller_flags: --max-reads-per-alignment-start 0 --do-not-run-physical-phasing --pileup-detection --dont-use-soft-clipped-bases
#
# --- End of NGS-Pipeline settings ---
#
#parameters
class: "parasite"
maxEE: "5,5"
trim_right: "10,10"
min_length: 30
truncQ: "5,5"
max_consist: 10
omegaA: 1e-120
justconcat: 0
platform: "PE"
trimqv: 15
#refs0
fasta: refs/Microhaps_Inserts_wMito.fasta
primer_fw: refs/microhap_pr_fwd.min_overlap.fasta
primer_rev: refs/microhap_pr_rv.min_overlap.fasta
mit_reference: refs/MIT/mit_synthetic_genome.fasta
mit_bedfile: refs/MIT/mit_synthetic_genome.bed
mit_ref_spec: refs/MIT/mit_spec2.fasta
# EOF