If you use this software, please cite these papers:
Yuan S, Johnston HR, Zhang G, Li Y, Hu Y-J, Qin ZS (2015) One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. PLoS Comput Biol 11(8): e1004448. doi:10.1371/journal.pcbi.1004448
Download citation (Right click -> Save as...):
- refEditor.ris (compatible with EndNote, Reference Manager, ProCite, RefWorks)
- refEditor.bib (compatible with BibDesk, LaTeX)
Shuai Y, Zhaohui Q: Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression. In Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on; 4-7 Oct. 2012. 2012: 718-724.
Download citation (Right click -> Save as...):
- diploid_mapping.ris (compatible with EndNote, Reference Manager, ProCite, RefWorks)
- diploid_mapping.bibtex (compatible with BibDesk, LaTeX)
Shuai Yuan, Email: [shuaiyuan.emory@gmail.com]
Please use the panel on the right to download source code.
Not provided.
CPU 2.0G Hz
Memory 8 GB
Hard disk 50 GB free space
Linux 64-bit or MacOS 64-bit, gcc, Read Mapping Tools (e.g. BWA or Bowtie).
This software package is to improve read mapping accuracy for diploid individuals.
It has two major programs: DiploidConstructor and MappingConvertor.
DiploidConstructor converts a haploid reference genome to a diploid reference genome according to the genotypes and sequencing read length.
MappingConvertor converts the SAM file created from being mapped to a diploid reference genome to being mapped to a haploid reference genome according to a dipmap file.
DiploidConstructor should be executed before calling read mapping tools (BWA, Bowtie etc.).
MappingConvertor should be executed after calling read mapping tools.
Download and uncompress this software, and then:
cd refeditor-master
make
then you can copy compiled executables to anywhere in your PATH variable ( e.g ~/bin/ ).
Usage:
DiploidConstructor -r haploid.fa -g genotypes -l length -o diploid.fa
Convert haploid reference genome to diploid reference genome according to the genotypes and sequencing read length
Example:
./DiploidConstructor -r hg19.fa -g known.genotypes -l 36 -o diploid.fa
Parameters (mandatory):
-r haploid reference genome file
-g genotypes file
-l read length
-o output diploid reference genome file
Parameters (optional):
-d maximal deletion in a read and mapped to alternative alleles [default=0]
-s sex of the individual [default="m"]
Usage:
MappingConvertor -i input.sam -m dipmap -o output.sam
Convert the sam file created from being mapped to a diploid reference genome to being mapped to a haploid reference genome according to a dipmap file.
Example:
./MappingConvertor -i input.sam -m hg19.di.fa.dipmap -o output.sam
Parameters (mandatory):
-i input SAM file
-m dipmap file created by DiploidConstructor
-o output SAM file
-
Compile
cd refeditor-master make -
Create genotypes file for target individual
./vcf2genotypes test.vcf NA19238 > test.genotypes -
Create customized reference genome
./DiploidConstructor -r hg19test.fa -g test.genotypes -l 36 -o hg19test.di.faThat will create two files: hg19test.di.fa and hg19test.di.fa.dipmap
-
Map the reads against the diploid reference genome using BWA (Version: 0.7.5a-r405)
Create index for reference genome
bwa index -a bwtsw hg19test.di.faPerform alignment
bwa aln hg19test.di.fa test.fastq > test.sai bwa samse -n 16 hg19test.di.fa test.sai test.fastq > test.sam -
Convert intermediate SAM file to final result SAM file
./MappingConvertor -i test.sam -m hg19test.di.fa.dipmap -o test.final.sam
Done! Now the reads in the test.fastq file are mapped successfully and stored in test.final.sam file.
- Map the reads against the haploid reference genome using BWA (Version: 0.7.5a-r405)
1.1 Create index for reference genome
bwa index -a bwtsw hg19test.fa
1.2 Make alignment
bwa aln hg19test.fa test.fastq > test.ha.sai
bwa samse -n 16 hg19test.fa test.ha.sai test.fastq > test.ha.sam
Done! Now the mapping results are stored in test.ha.sam file. By viewing this file, you will find the mapping quality is 0 for all reads. That's because traditional method does not take into account the genotypes information
Minor bugs fixing
Add test.vcf and vcf2genotypes
Update the example
Add files that are needed in the example Create release tags automatically
First working release