Using BSA mixed pool sequencing data for ED analysis and plotting
- Backgroud
- Install
- Usage
- Example
- Output
- License
https://github.com/xiaodaidaidai/ED.git
usage: BSA_ED.py [-h] -vcf VCF -bulk1 BULK1 -bulk2 BULK2 [-power POWER] [-minDP MINDP] [-maxDP MAXDP] [-window WINDOW] [-step STEP] -outpre OUTPRE
Calculate ED power from VCF file
options:
-h, --help show this help message and exit
-vcf VCF Input VCF file
-bulk1 BULK1 Sample name for bulk1
-bulk2 BULK2 Sample name for bulk2
-power POWER ED power (default is 5)
-minDP MINDP Minimum depth of variation (per sample) (default is 4)
-maxDP MAXDP Maximum depth of variation (per sample) (default is 250)
-window WINDOW Window size (kilobases) (default is 2000)
-step STEP Step size (kilobases) (default is 100)
-outpre OUTPRE Output file prefix
usage: BSA_ED_sliding.R [--] [--help] [--opts OPTS] ED window chr
threshold outpre
Mapping the distribution of ED correlation values on chromosomes
positional arguments:
ED Input: ED.tsv
window Input: sliding_window.tsv
chr Input: Chromosome list file (chr.len)
threshold Input: Threshold of confidence interval (99 or 95)
outpre Output prefix
flags:
-h, --help show this help message and exit
optional arguments:
-x, --opts RDS file containing argument values
usage: BSA_ED_loess.R [--] [--help] [--opts OPTS] ED chr threshold
outpre
Generate ED figure
positional arguments:
ED Input: ED.tsv
chr Input: Chromosome length file (chr.len)
threshold Input: Threshold of confidence interval (99 or 95)
outpre Output prefix
flags:
-h, --help show this help message and exit
optional arguments:
-x, --opts RDS file containing argument values
usage: vcf_processor.py [-h] input_file output_file
Process VCF file and generate output
positional arguments:
input_file Input VCF file
output_file Output file
options:
-h, --help show this help message and exit
python BSA_ED.py \
-vcf all.clean.snp.qtlseq.vcf \
-bulk1 S-pool -bulk2 T-pool \
-power 5 \
-minDP 4 -maxDP 100 \
-outpre all.clean.snp.BSA-ED
Rscript BSA_ED_sliding.R \
all.clean.snp.BSA-ED.snp_EDpower5.tsv \
all.clean.snp.BSA-ED.sliding_EDpower5.tsv \
chr.len \
99 \
all.clean.snp.BSA-ED5
Rscript BSA_ED_loess.R \
all.clean.snp.BSA-ED.snp_EDpower5.tsv \
chr.len \
99 \
all.clean.snp.BSA-ED5