Parameter File Generation for PAPipe
Load parameters for test data
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Documentation
Global parameters
(1) Reference genome assembly file:
(2) Reference dbSNP file (optional):
(3) Total number of chromosomes in the reference genome:
(4) Number of autosomes in the reference genome:
(5) Names of sex chromosomes in the reference genome (optional):
(6) Name of output directory:
(7) Threads:
Population setting
Insert the names of populations
Begin analysis from
From read QC (you have raw reads)
From read mapping (you have trimmed reads)
From variant calling (you have read mapping files)
From population genetic analyses (you have variant calling results)
Input file setting
Input file setting
Input file setting
Input file setting
Input variant file name (Gzipped VCF is required)
Input sample list
Population setting for input files
You can select rows in a range at once
by first clicking the first row and then shift-clicking the last row in the range.
Sample name
Sample file
Population
Sex
Select population
Apply population
Female
Male
None
Apply sex
Read QC
<manual>
(1) Quality (INT):
(2) Minimum-length (INT):
Additional user parameters (optional)
TrimGalore:
# -m and -k are already set
Read alignment
BWA
<manual>
Bowtie 2
<manual>
Additional user parameters (optional)
BWA mem:
# -t is already set
Bowtie 2:
# -p, -x, -1, -2, and -S are already set
Variant calling
GATK3
<manual>
GATK4
<manual>
BCFtools
<manual>
Additional user parameters (optional)
GATK3 IndelRealigner:
GATK3 BaseRecalibrator:
GATK3 HaplotypeCaller:
GATK3 VariantFiltration:
# -I, -o, -R, —targetIntervals, and --fix_misencoded_quality_scores are already set
# -I, -o, -R, -nct, and -knownSites are already set
# -I, -o, -R, -nct, -ERC, -variant_index_type and parameter are already set
# Enter filterExpression
GATK4 BaseRecalibrator:
GATK4 ApplyBQSR:
GATK4 HaplotypeCaller:
GATK4 VariantFiltration:
# -I, -O, -R and --known-sites are already set
# -I, -O, -R and --known-sites are already set
# -I, -O, -R, -ERC and --native-pair-hmm-threads are already set
# Enter filterExpression
BCFtools call:
# -c, -v, --output-type and —threads are already set
Post processing
(1) Geno
<manual>
:
(2) Maf
<manual>
:
(3) Hwe
<manual>
:
Population genetic analysis
Check for all
Principal component analysis by GCTA
<manual>
(1) Number of PC:
(2) Objective sum of the proportion of variance explained (%):
(3) Max PC (Maximum PC when making the pairwise PC combinations):
# Only autosomal chromosomes are used
Principal component analysis by PLINK v 2.0
<manual>
(1) Number of PC:
(2) Objective sum of the proportion of variance explained (%):
(3) Max PC (Maximum PC when making the pairwise PC combinations):
(4) Do not use non-autosomal chromosomes:
Phylogenetic tree analysis
<manual>
(1) m (MAF_threshold):
(2) M (Missing_rate):
(3) l (LD_threshold):
Population tree analysis
<manual>
(1) m (maximum number of migration edges to add):
(2) k (number of SNPs per block for estimation of covariance matrix):
(3) LD pruning threshold:
Additional user parameters (optional)
# -m and -k are already set
Population structure analysis
<manual>
(1) k (maximum number of ancestors):
Linkage disequilibrium decay analysis
<manual>
(1) MaxDist (bp) (ex: 500,1000,5000,10000):
Selective sweep analysis
<manual>
(1) Grid point spacing (bp):
(2) Do not use non-autosomal chromosomes:
Population admixture analysis
<manual>
Multiple sequentially Markovian coalescent analysis
<manual>
(1) i (number of iterations):
(2) r (initial ratio of recombination over mutation rate):
(3) p ("1*2+25*1+1*2+1*3" # pattern of fixed time segments):
Pairwise sequentially Markovian coalescent analysis
<manual>
(1) q (rounds of iterations):
(2) N (maximum number of iterations):
(3) t (maximum 2N0 coalescent time):
(4) r (initial theta/rho ratio):
(5) p ("4+252+4+6" # pattern of parameters):
Fixation index analysis
<manual>
(1) window size (bp):
(2) window step (bp):
(3) genomewideLine:
Additional user setting for population combinations (optional)
Population group 1
Option 1
Option 2
Option 3
Population group 2
Option 1
Option 2
Option 3
Generate parameter files
Generate parameter files
Generate parameter files
Generate parameter files