To use "BWA" to align sequencing reads to the reference genome

Codes

Run single-end

bwa mem <ref_genome.fasta> <sample.R1.fq> > <alignment.sam>

Run paired-end

bwa mem <ref_genome.fasta> <sample.R1.fq> <sample.R2.fq> > <alignment.sam>

References

BWA

To use "GATK" to call the variants

Codes

Map reads to the genome

gatk HaplotypeCaller -R <ref_GENOME.fasta> -I <output.bam> -O <output.gatk.vcf>

References

GATK

To use "SnpEff" to conduct the variant annotations and functional effect prediction

Codes

Run SnpEff java script

java -Xmx8g -jar snpEff.jar -v <ref_genome> <sample_variant.vcf> > <sample_variant_annotation.vcf>

References

SnpEff

IMB Bioinformatics Core Pipeline: bbsc_portal

fastp -w 16 -h sample.fastp.html -j sample.fastp.json -i ./ -o clean_read.fastq
bwa mem -t 16 path_to_bwa_index/ref clean_read.fastq | samtools sort -@ 16 -O BAM -o sample.sorted.bam -
java -jar picard.jar MarkDuplicates -I sample.sorted.bam -O sample.mark.bam -M sample.metrics.txt -ASSUME_SORTED -VALIDATION_STRINGENCY LENIENT
java -jar picard.jar AddOrReplaceReadGroups -I sample.mark.bam -O sample.rg.bam -RGID 1 -RGLB lib1 -RGPL illumina -RGPU unit1 -RGSM MyRead
java -jar picard.jar BuildBamIndex -I sample.rg.bam
gatk HaplotypeCaller --native-pair-hmm-threads 16 -R ref.fa -I sample.rg.bam -O sample.gatk.vcf
java -Xmx8g -jar snpEff.jar ref.fa sample.gatk.vcf > sample.gatk.vcf.SnpEff