Contamination Source Predictor（ConSPr）: A software for contamination purity estimation, contamination genotype prediction, and contamination source tracing
ConSPr is a fast and robust method designed for cross-individual contamination level estimation, contamination source genotype inference and contamination source finding in customized panel experiments. Importantly, our method of estimating contamination in the tumor samples is not affected by copy number changes and is able to detect contamination levels as low as 1%,and When the pollution source is a single sample and the pollution proportion exceeds 5%, the pollution source can be accurately identified.
- Version: 1.0.0
- Author: cailili
- Contact: lilicai@chosenmedtech.com
Required input files: two bam files (tumor, normal)
Required software: GATK 3 and GATK 4 , Conpair,python 3 , scipy, numpy, pandas,java
Required data: Human genome file (GRCh37,GRCh38) ,bed,dbsnp
GRCh37:
The fasta file can be downloaded from: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
In order to be able use the fasta file as a reference 2 additional files are required:human_g1k_v37.dict, human_g1k_v37.fa.fai
To create these files please follow: http://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
The dbSNP file can be download from: ftp:/gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/dbsnp 138.hg19.vcf.gz
GRCh38:
The fasta file can be downloaded from: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
In order to be able use the fasta file as a reference 2 additional files are required:hg38.dict, hg38.fa.fai
To create these files please follow: http://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
The dbSNP file can be download from:ftp:/gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_138.hg38.vcf.gz
Dependencies:
- perl 5.28.1 or higher
- python 3.8.8 or higher
- numpy 1.7.0 or higher
- scipy 0.14.0 or higher
- pandas 1.2.4 or higher
- GATK 3.7
- GATK 4.1.9.0 or higher
- java 1.8.0_202 or higher
- conpair [https://github.com/nygenome/Conpair]
Modify Configuration file:
vi ConSPr/bin/Config_Contamination.txt
PERL = ${your_perl}
PYTHON3 = ${your_python3}
JAVA=${your_java}
gatk=${your_gatk3}
GATK=${your_gatk4}
ref=${your_genome_dir}/human_g1k_v37.fasta
ref_fai=${your_genome_dir}/human_g1k_v37.fasta.fai
ref_dict=${your_genome_dir}/human_g1k_v37.dict
ref_2bit=${your_genome_dir}/human_g1k_v37.fasta.2bit
realign_599=${your_file_dir}/align.bed
realign_autoChr=${your_file_dir}/autoChr.bed
dbsnp=${your_file_dir}/dbsnp_138.hg19.vcf
baseline=${your_file_dir}/compair.vcf
Write Samplelist: In order to ensure that the input bam file can be found, please link the bam file to a directory, and the bam file suffix is sample_T.rmdup.sort.bam
序号 订单编号 样本编号_肿瘤 样本编号_对照
1 Prefix_N Sample_T Sample_N
Most common usage and additional options:
To run ConSPr:
$(python3) ${ConSPr}/bin/MainProcess.py --outdir ${outdir} --libsampleinfo Samplelist --bamdir ${bam_dir} --name 20231030
Optional:
--help show help message and exit
--outdir OUTDIR Output Dir[Required]
--libsampleinfo LIBSAMPLEINFO Laboratory sample information sheet
--cpu CPU The maximum number of samples to be delivered.
--name NAME project name
Searching for sources of contamination in a library of candidate contamination samples:
${python3} ${ConSPr}/bin/Source/find.py --outdir ${outdir} --baseline ${baseline} --prefix ${prefix} --pollution ${pollutionfile} --indir ${candidate_database} --pollutionCutoff ${pollutioncutoff}
Optional:
--help show help message and exit
--outdir OUTDIR Outdir
--baseline BASELINE Dir of model file
--prefix PREFIX file name
--pollution POLLUTION Pollution_Genetype_file
--indir INDIR normal germline files
--pollutionCutoff POLLUTIONCUTOFF pollution sources cutoff default 0.9
Contamination
An example of a contamination file can be viewed here: ([`contamination.stat.xls`](${ConSPr}/example/sample1/sample1/Pair/Contamina/Conpair/sample1_contamination.stat.xls)).
Contamination Genotype
An example of a genetype file can be viewed here: ([`pollution.change.genetype.xls`](ConSPr/example/sample1/sample1/Pair/Genotype/sample1.sample.pollution.change.genetype.xls)).
Contamination Source
An example of a pollution sample source file can be viewed here: ([`pollution.source_result.xls`](ConSPr/example/sample1/source/sample.pollotion.source_result.xls)).