OryzaSNP_pipeline

A description of the analysis step of Oryza sativa variant calling pipeline.

Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice.

Yabe S, Yoshida H, Kajiya-Kanegae H, Yamasaki M, Iwata H, Ebana K, Hayashi T, Nakagawa H.
PLoS One. 2018 Nov 20;13(11):e0207627.
doi: 10.1371/journal.pone.0207627. PMID: 30458025
Pipeline LINK

Choosing the optimal population for a genome‐wide association study: A simulation of whole‐genome sequences from rice

Kosuke Hamazaki Hiromi Kajiya‐Kanegae Masanori Yamasaki Kaworu Ebana Shiori Yabe Hiroshi Nakagawa Hiroyoshi Iwata The Plant Genome. 2020;e20005. doi.org/10.1002/tpg2.20005
Pipeline LINK

Coupling day length data and genomic prediction tools for predicting time-related traits under complex scenarios

Diego Jarquin, Hiromi Kajiya-Kanegae, Chen Taishen, Shiori Yabe, Reyna Persa, Jianming Yu, Hiroshi Nakagawa, Masanori Yamasaki, Hiroyoshi Iwata Sci Rep. 2020 A10:13382. doi: 10.1038/s41598-020-70267-9.
PMID: 32770083
Pipeline LINK

Predicting Rice Heading Date Using an Integrated Approach Combining a Machine Learning Method and a Crop Growth Model

Tai-Shen Chen, Toru Aoike, Masanori Yamasaki, Hiromi Kajiya-Kanegae and Hiroyoshi Iwata Front Genet. 2020 11:599510. doi: 10.3389/fgene.2020.599510
PMID: 33391352
Pipeline LINK

---

Analysis workflow for detection of genome-wide variations in TASUKE+ of RAP-DB was modified.

REF=RGSP-1.0 genome (including organella and unanchored contig sequences) FASTA

trimmomatic (v0.38)

$ java -jar trimmomatic-0.38.jar PE
-phred33 read.r1.fastq.gz read.r2.fastq.gz
read.pe.r1.fastq.gz read.se.r1.fastq.gz read.pe.r2.fastq.gz read.se.r2.fastq.gz
ILLUMINACLIP:adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 MINLEN:30

Mapping / bwa v0.7.17

$ java -jar picard.jar FastqToSam
FASTQ=read.pe.r1.fastq.gz
FASTQ2=read.pe.r2.fastq.gz
OUTPUT=uBAM.bam
READ_GROUP_NAME=${SAMPLE_ID}
SAMPLE_NAME=${SAMPLE_ID}
LIBRARY_NAME=${SAMPLE_ID} \

$ java -jar picard.jar MergeBamAlignment
ALIGNED=alignment.sort.bam
UNMAPPED=uBAM.bam
OUTPUT=alignment.merge.bam
REFERENCE_SEQUENCE=genome.fa

samtools flagstat / samtools (v1.9)

$samtools flagstat "$dir2"/"$name".sorted.bam > "$dir3"/"$name"_flagstat.txt

FixMate information / picard-tools-2.5.0

java -jar picard.jar FixMateInformation I="$dir2"/"$name".sorted.bam O="$dir5"/"$name".fxmt.bam SO=coordinate CREATE_INDEX=TRUE

Remove PCR duplicates / Picard (v2.18.17)

$ java -jar picard.jar MarkDuplicates
INPUT=alignment.merge.bam
OUTPUT=alignment.rmdup.bam
METRICS_FILE=rmdup.matrix
REMOVE_DUPLICATES=true
MAX_RECORDS_IN_RAM=1000000
TMP_DIR=./tmp $ samtools index alignment.rmdup.bam

Variant detection and filtering by GATK / GATK (v4.0.11.0)

$ gatk HaplotypeCaller
--input alignment.rmdup.bam
--output variants.g.vcf.gz
--reference genome.fa
-max-alternate-alleles 2
--emit-ref-confidence GVCF

GenomicsDBImport

array=(chr01 chr02 chr03 chr04 chr05 chr06 chr07 chr08 chr09 chr10 chr11 chr12)

for name in ${array[@]}; do echo $name; gatk --java-options "$JAVA_MEM" GenomicsDBImport --reference genome.fa -V variants_A.g.vcf.gz -V variants_B.g.vcf.gz -V variants_C.g.vcf.gz --genomicsdb-workspace-path variants_"$name" --intervals "$name" done

GenotypeGVCFs

for name in ${array[@]}; do echo $name; gatk --java-options "$JAVA_MEM" GenotypeGVCFs --reference genome.fa -V gendb://variants_"$name" -G StandardAnnotation --new-qual -O variants.genotype_"$name".vcf.gz done

VariantFiltration

for name in ${array[@]}; do echo $name; gatk --java-options "$JAVA_MEM" VariantFiltration --reference genome.fa --variant variants.genotype_"$name".vcf.gz --output variants.filter.genotype_"$name".vcf.gz --filter-expression "QD < 5.0 || FS > 50.0 || SOR > 3.0 || MQ < 50.0 || MQRankSum < -2.5 || ReadPosRankSum < -1.0 || ReadPosRankSum > 3.5" --filter-name "FILTER" done

SelectVariants

for name in ${array[@]}; do echo $name; gatk --java-options "$JAVA_MEM" SelectVariants --reference genome.fa --variant variants.filter.genotype_"$name".vcf.gz --output variants.varonly.vcf.gz --exclude-filtered --select-type-to-include SNP --select-type-to-include INDEL done

merge varonly.vcf

java $JAVA_MEM -jar $PICARD_HOME/picard.jar MergeVcfs O=variants.varonly.vcf.gz I= variants_chr01.varonly.vcf.gz I=variants_chr02.varonly.vcf.gz I= variants_chr03.varonly.vcf.gz I=variants_chr04.varonly.vcf.gz I= variants_chr05.varonly.vcf.gz I=variants_chr06.varonly.vcf.gz I= variants_chr07.varonly.vcf.gz I=variants_chr08.varonly.vcf.gz I= variants_chr09.varonly.vcf.gz I=variants_chr10.varonly.vcf.gz I= variants_chr11.varonly.vcf.gz I= variants_chr12.varonly.vcf.gz