Wrap-up R package to coordinate SimusCop simulations.
Also, here we present a easy conversion of VCF files in variations and snp files for SimuSCoP simuReads. This tools is useful if you want to simulate Illumina reads based on empirical variations already stored in a VCF file.
Install from GitHub:
library(devtools)
install_github("Cristianetaniguti/simuscopR")
It also requires samtools installed.
Or use the Docker image:
docker pull cristaniguti/simuscopr:latest
All inputs must have information for just one chromosome and one sample.
- Reference genome and indexes from picard, bwa and samtools
- Sorted BAM file from real data
- VCF file
- BED file
If you need to filter the files to keep only one chromosome, we suggest:
docker run -v $(pwd):/opt cristaniguti/r-samtools samtools view -b /opt/your_bam_file Chr10 > filtered_bam
docker run -v $(pwd):/opt cristaniguti/vcftools vcftools --gzvcf /opt/vcf.file.gz --indv ID1 --chr Chr01 --recode --out vcf_filt
To obtain the BED file from the BAM file
docker run -it -v $(pwd):/data biocontainers/bedtools:v2.28.0_cv1 bamtobed -i /data/PT_F.chr.sorted.bam > /data/PT_F.sorted_filt.bed
docker run -it -v $(pwd):/opt cristaniguti/simuscopr
You can find these test files here system.file("extdata", package="simuscopR")
.
setwd("/opt")
seqToProfile("PT_F.chr.sorted.bam", "PT_F.sorted_filt.bed", "gatk_chr10_PT_F.recode.vcf",
"reference/Chr10.populus.fa", "PT_F.profile")
library(vcfR)
vcfR.object <- read.vcfR("gatk_chr10_PT_F.recode.vcf")
variants <- vcf2variants(vcfR.object, sample = "PT_F", chrom = "Chr10")
write.table(variants$SNVs, file = "SNVs.txt", sep = "\t", quote = F, col.names = F, row.names = F)
write.table(variants$indels, file = "indels.txt", sep = "\t", quote = F, col.names = F, row.names = F)
write.table(variants$insertions, file = "insertions.txt", sep = "\t", quote = F, col.names = F, row.names = F)
system("cat SNVs.txt indels.txt insertions.txt > variants.txt")
simuReads(ref = "reference/Chr10.populus.fa",
profile = "PT_F.profile",
variation = "variants.txt",
target = "PT_F.sorted_filt.bed",
name = "PT_F",
output = ".",
layout = "SE",
threads = 6,
verbose = 1,
coverage = 15)
docker run -v $(pwd):/data kfdrc/bwa-picard:latest-dev bin/bwa mem -t 2 \
/data/reference/Chr10.populus.fa /data/PT_F.fq > file.bam
docker run -v $(pwd):/data kfdrc/bwa-picard:latest-dev java -jar /picard.jar SortSam \
I="/data/file.bam" \
O="/data/PT_F.simulated.bam" \
TMP_DIR=./tmp \
SORT_ORDER=coordinate \
CREATE_INDEX=true
# Check images on IGV