001、
(base) [root@PC1 test]# cat step1.slurmdocker run --rm -v $PWD:/data quay.io/biocontainers/fastp:0.24.1--heae3180_0 \ fastp \ -i /data/SRR1770413_1.fastq \ -I /data/SRR1770413_2.fastq \ -o /data/sample.clean.R1.fastq.gz \ -O /data/sample.clean.R2.fastq.gz \ -h /data/fastp.html \ -j /data/fastp.json \ -w 4 > xxx.txt 2>&1
002、
(base) [root@PC1 test]# cat step2.slurmdocker run --rm -v $PWD:/data -v /home/ref:/ref quay.io/biocontainers/bwa:0.7.17--hed695b0_6 bwa mem -t 16 -M -R "@RG\tID:SRR1770413\tPL:illumina\tSM:SRR1770413" /ref/GCF_000005845.2_ASM584v2_genomic.fna /data/SRR1770413_1.fastq /data/SRR1770413_2.fastq > ./SRR1770413.sam
003、
(base) [root@PC1 test]# cat step3.slurmdocker run --rm -v $PWD:/data quay.io/biocontainers/samtools:1.23--h96c455f_0 samtools view -bS /data/SRR1770413.sam > ./SRR1770413.bam
004、
(base) [root@PC1 test]# cat step4.slurmdocker run --rm -v $PWD:/data quay.io/biocontainers/samtools:1.23--h96c455f_0 samtools sort /data/SRR1770413.bam > SRR1770413.sorted.bam
005、
(base) [root@PC1 test]# cat step5.slurmdocker run --rm -v $PWD:/data -w /data quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1 gatk --java-options "-Xmx2g -Xms2g -XX:+UseSerialGC" MarkDuplicates -I SRR1770413.sorted.bam -O SRR1770413.sorted.markdup.bam -M SRR1770413.sorted.markdup_metrics.txt
006、
(base) [root@PC1 test]# cat step6.slurmdocker run --rm -v $PWD:/data quay.io/biocontainers/samtools:1.23--h96c455f_0 samtools index /data/SRR1770413.sorted.markdup.bam
007、
(base) [root@PC1 test]# cat step7.slurmdocker run --rm -v $PWD:/data -v /home/ref:/ref \quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1 gatk HaplotypeCaller \-R /ref/GCF_000005845.2_ASM584v2_genomic.fna --emit-ref-confidence GVCF \-I /data/SRR1770413.sorted.markdup.bam \-O /data/sample_name.g.vcf.gz
。