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OryzaSNP_pipeline

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

PLoS One. 2018 Nov 20;13(11):e0207627.

REF=IRGSP-1.0_genome.fasta

trimmomatic

java -jar trimmomatic-0.36.jar PE -threads 4 -phred33 "$dir"/"$name"_1.fastq.gz "$dir"/"$name"_2.fastq.gz "$dir"/"$name"_1_paired.fastq.gz "$dir"/"$name"_1_unpaired.fastq.gz "$dir"/"$name"_2_paired.fastq.gz "$dir"/"$name"_2_unpaired.fastq.gz ILLUMINACLIP:/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Mapping / bwa-0.7.12

$bwa mem -M -t 4 oryza_index "$dir"/"$name"_1_paired.fastq.gz "$dir"/"$name"_2_paired.fastq.gz | $samtools view -bS - | $samtools sort -T tmpsam"$name" -@4 -o "$dir2"/"$name".sorted.bam

samtools flagstat / samtools-1.3.1

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

sort_bam index

$samtools index "$dir2"/"$name".sorted.bam

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

Mark duplicate reads

java -jar picard.jar MarkDuplicates I="$dir5"/"$name".fxmt.bam O="$dir5"/"$name".mkdup.bam M="$dir5"/"$name".metrics.txt CREATE_INDEX=TRUE

Add or replace read groups

java -jar picard.jar AddOrReplaceReadGroups I="$dir5"/"$name".mkdup.bam O="$dir5"/"$name".addrep.bam RGPL=illumina RGLB=lib1 RGPU=unit1 RGSM="$name" RGID="$name"

$samtools index "$dir5"/"$name".addrep.bam

GATK RealignerTargetCreator / GATK 3.7-0-gcfedb67

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $REF -I "$dir5"/"$name".addrep.bam -o "$dir5"/"$name".addrep.intervals

GATK IndelRealigner

java -jar GenomeAnalysisTK.jar -T IndelRealigner -R $REF -I "$dir5"/"$name".addrep.bam -targetIntervals "$dir5"/"$name".addrep.intervals -o "$dir5"/"$name".realn.bam

CollectRawWgsMetrics

java -jar picard.jar CollectRawWgsMetrics I="$dir5"/"$name".realn.bam O="$dir6"/"$name"_metrics.txt R=$REF INCLUDE_BQ_HISTOGRAM=true

SNP call

java -Xmx8g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -I "$dir5"/"$name".realn.bam -R $REF -glm BOTH -gt_mode DISCOVERY -o $name.vcf -nt 4