Tutorial of ggComp
ggComp (Genomic-based Germplasm Compare) is a novel strategy fitting complex genomes to evaluate germplasm resources by identifying shared genomic regions and excluding pervasive copy number variations for pairwise accessions.
Installation
ggComp is a light weight software that only need to make sure Python 3.8.5, samtools 1.4 and bcftools 1.9 are well installed and set in environment path.
Clone the ggComp repository
git clone https://github.com/zack-young/ggComp.gitUsage
Program: ggComp (A pairwised comparison method to identify similar genetic regions and shared CNV regions between accessions.)
Version: 1.0
Usage: ggComp [-v|--version] [-h|--help] <command> <argument>
Commands:
CNV_detector detect CNV regions
SNP_extractor extract SNP information from VCF
DSR_counter compute the DSR
SGR_PHR_definer identify SGR and PHR
HMM_smoother smoothing SGR and PHR result using HMMCNV_detector
detect CNV regions
Usage: ggComp CNV_detector <--chr_lis <STRING>> <--single_CNV <FILE> | --pair_CNV <FILE>>
--chr_lis <STRING> chromosomes that listed in behind file
e.g. 'chr1A chr1B chr1D'
Options:
--single_CNV detect CNV region of samples ::: input file contains chromosme
list, path of BED file, path of BAM file and output file
e.g. chromosome BED BAM output_dev
produce three files: *.mask_CNV
*.mask_CNV_deletion
*.mask_CNV_duplication
--pair_CNV identify pairwise sample specific CNV regions and shared CNV
regions::: input file contains sample names, path of CNV file
and path of output file directory
e.g. sample1_name sample1_directory sample2_name sample2_directory pair_dircetory
chromosome length in bed file shall not exceed the limit of bedtools (400Mb)
see test/single_CNV.config and test/pair_CNV.config for more details
(colunms separated by tab)SNP_extractor
extract SNP information from VCF for DSR calculation
Usage: ggComp SNP_extractor <--config <FILE>>
Options:"
--config <FILE> file contains path of vcf files, sample ID list in vcf for
extracting(separated by ','), path of output file
e.g. VCF_file vcf_ID output_file
see test/SNP_extractor.config for more details
(colunms separated by tab)DSR_counter
compute the DSR (Different SNP ratio) by bin
Usage: ggComp DSR_counter <--config <file>> [Options]
--config <FILE> file contains：path of files contain SNP inforamtion;
path of output files; end position of chromosomes
(use 'defalut' to call built-in end position of each chromosomes)
e.g. SNP_file output_file END\default
Options:
--DP_low <INT> exclude SNP with DP <= <int>. default 3
--DP_high <INT> exclude SNP with DP >= <int>. default 99
--GQ_sample <INT> exclude SNP with GQ <= <int>. default 8
--bin_size <INT> bln size. default 1000000
see test/DSR_counter.config for more details (colunms separated by tab)SGR_PHR_definer
detect SGR (Similar Genetic Regions) and PHR (Polymorphism Hotspot Regions) between sample pairs
Usage: ggComp SGR_PHR_definer <--noCNV <file> | --plus_CNV <file>> [Options]
--no_CNV <FILE> ignore CNV
file contains path of files contain DSR information
and path of output files.
e.g. DSR_file output
--plus_CNV <FILE> take CNV into consideration"
file contains path of files contain DSR information
path of CNV file and path of output files.
e.g. DSR_file CNV_file output
Options
--LEVEL <INT> threshold divide SGR and PHR. default 10
see test/SGR_PHR_definer.config for more details (colunms separated by tab)HMM_smoother
smoothing SGR (Similar Genetic Regions) and PHR (Polymorphism Hotspot Regions) result using HMM
Usage: ggComp HMM_smoother [Options]
Options:
--input <FOLDER> folder path of SGR and PHR phasing results
--output <FOLDER> output path
--folder_lis <FILE> containing a list of folder names of SGR and PHR phasing
results that are goining to be smoothed
e.g. C2_C10
C2_C10
--processes <INT> (optional) maximum worker processes"
default: 2"
--train (optional) train the model using input data (otherwise using"
the model published in the article)"
--niter <INT> (optional) maximum number of iterations to perform in training"
default: 60"Visualization
Plot the distribution of SGR PHR and CNV across whole genome
"Usage: ggComp Visualization <--config <FILE>>"
Options:
--config <FILE> file contains path of vcf files, sample ID list in vcf for"
extracting(separated by ','), path of output file"
e.g. path suffix SAMPLE1 SAMPLE1_name SAMPLE2 SAMPLE2_name pdf_path"
see test/plot.config for more details (colunms separated by tab)"Quickstart with an example
CNV_detector
This is the first step of ggComp that detect CNV regions through BAM files.
Each BAM file should contain only one chromosome and the chromosome name in first column of config file should consistent with that in BAM file.
BED file records bins that going to be processed.
Chromosomes that list in –chr_lis may not consistent with config file as chromosomes may be separated into parts in BAM file.
e.g. --chr_lis 'chr1A chr1B' but in config file is chr1A.1 chr1A.2 chr1B.2 chr1B.2.
single_CNV.config
chr1A test/CNV_detector/chr1A_11-12Mb.bed test/CNV_detector/C2/chr1A_11-12Mb_C10.bam test/CNV_detector/C10
chr1A test/CNV_detector/chr1A_11-12Mb.bed test/CNV_detector/C2/chr1A_11-12Mb_C2.bam test/CNV_detector/C2sh src/ggComp.sh CNV_detector --chr_lis chr1A --single_CNV test/single_CNV.configpair_CNV.config
C2 test/CNV_detector/C2 C10 test/CNV_detector/C10 test/CNV_detector/C2_C10sh src/ggComp.sh CNV_detector --chr_lis chr1A --pair_CNV test/pair_CNV.configSNP_extractor
extract SNP information from VCF, including ‘CHROM POS REF ALT GT DP GQ’ only biallele by MAF<0.01.
SNP_extractor.config
test/SNP_extractor/chr1A_11-12Mb.bcf 2-90377,10-83979 test/SNP_extractor/chr1A_11-12Mb.SNP_gtsh src/ggComp.sh SNP_extractor --config test/SNP_extractor.configDSR_counter
compute the DSR from SNP by bins (default bin length: 1000000bp)
DSR_counter.config
test/SNP_extractor/chr1A_11-12Mb.SNP_gt test/DSR_counter/chr1A_11-12Mb.DSR 12000000sh src/ggComp.sh DSR_counter --config test/DSR_counter.configSGR_PHR_definer
identify SGR and PHR from DSR file
SGR_PHR_plus_CNV.config
test/DSR_counter/chr1A_11-12Mb.DSR test/CNV_detector/C2_C10/chr1A.C2toC10all_CNV test/SGR_PHR_definer/chr1A_11-12Mb_combineCNV.levelsh src/ggComp.sh SGR_PHR_definer --plus_CNV test/SGR_PHR_plus_CNV.configSGR_PHR_noCNV.config
test/DSR_counter/chr1A_11-12Mb.DSR test/SGR_PHR_definer/chr1A_11-12Mb_noCNV.levelsh src/ggComp.sh SGR_PHR_definer --no_CNV test/SGR_PHR_noCNV.configHMM_smoother
smoothing SGR and PHR result using HMM #### Smooth only
sh WheatComp.sh HMM_smoother \
-i /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/data \
--folder_lis /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/folders.txt \
-o /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/out\
--processes 21Train & Smooth
sh WheatComp.sh HMM_smoother \
-i /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/data \
--folder_lis /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/folders.txt \
-o /data3/user3/wangwx/projs/HMM_for_yzz_comp/210328-modify/test/out \
--processes 21 \
--train \
--niter 30Visualization
SGR_PHR_noCNV.config
test/Visualization .homo_undefined_snp_level.HMMv1 Zang1817 Zang1817 S14 ZXM1341 test/Visualizationsh src/ggComp.sh Visualization --config test/Visualization.config