SNP Calling: GATK

SNP Calling: GATK

1. build bwa index

bwa index genome.fna
##Exp:
bwa index Apostichopus_japonicus.fna

2. reads Mapping

bwa mem -t 4 -R '@RG\tID:foo\tPL:illumina\tSM:E.coli_K12' genome.fna reada_1.fq reads_2.fq | samtools view -Sb - > bwa.bam

##Exp:
bwa mem -t 4 -R '@RG\tID:foo\tPL:illumina\tSM:E.coli_K12' Apostichopus_japonicus.fna SRR771602.fastq | samtools view -Sb - > AJ.bam

3. sort by samtools

samtools sort bwa.bam -o bwa.sorted.bam > bwa.sorted.bam
samtools faidx genome.fna

##Exp:
samtools sort AJ.bam -o AJ.sorted.bam > AJ.sorted.bam
##Exp:
samtools faidx Apostichopus_japonicus.fna

4. Maker PCR repeats

gatk MarkDuplicates -I bwa.sorted.bam -O bwa.sorted.markdup.bam   -M bwa.sorted.markdup_metrics.txt

##Exp:
gatk MarkDuplicates -I AJ.sorted.bam -O AJ.sorted.markdup.bam   -M AJ.sorted.markdup_metrics.txt

samtools index bwa.sorted.markdup.bam

5. Prepare a dict file

gatk CreateSequenceDictionary -R genome.fna -O genome.dict

##Exp:
gatk CreateSequenceDictionary -R Apostichopus_japonicus.fna -O Apostichopus_japonicus.dict

6. Build intermidia file, gvcf file

gatk HaplotypeCaller -R genome.fna --emit-ref-confidence GVCF -I bwa.sorted.markdup.bam -O  bwa.g.vcf

##Exp:
gatk HaplotypeCaller -R Apostichopus_japonicus.fna --emit-ref-confidence GVCF -I AJ.sorted.markdup.bam -O  AJ.g.vcf

7. Finally

gatk GenotypeGVCFs -R genome.fna -V bwa.g.vcf -O bwa.vcf

##Exp:
gatk GenotypeGVCFs -R Apostichopus_japonicus.fna -V AJ.g.vcf -O AJ.vcf

Another Example:

炎季宏, 2018