HISAT2 pipeline

mapping

/data1/program/hisat2/hisat2-2.2.1/hisat2 -q --phred33 -x /data1/ref/Gmax_275_v2.0.fa.hisat --summary-file SS2-2_1_hisat_summary -p 6 -1 {forward_input.fq.gz} -2 {reverse_input.fq.gz} | samtools view -bS -q30 > {output}.bam

sort/markdup

samtools sort {hisat.bam} -o {hisat.sort.bam}
java -jar /data1/program/picard-2.23.4/picard/build/libs/picard.jar MarkDuplicates I={hisat.sort.bam} O={hisat.sort.mkdup.bam} M={hisat.mkdup.metrics}