python /mnt/wigstore3/user/kendall/stillman05/add.varietal.tag01.hisat2_sc3.bypair.py <(gunzip -c <FASTQ1>) <(gunzip -c <FASTQ2>) <(samtools view -h /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP2>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam) 1 | samtools view -Sbh - > /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP2>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.vt.bypair.bam

samtools index /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP2>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.vt.bypair.bam