python /mnt/wigstore5/user/kendall/wigstore2/stillman03/add.varietal.tag01.hisat2_sc3.bypair.py <(gunzip -c /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/s_<LANE>_1_sequence.b<BARCODE>.txt.gz) <(gunzip -c /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/s_<LANE>_2_sequence.b<BARCODE>.txt.gz) <(samtools view -h /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam) 1 | samtools view -Sbh - > /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.vt.bypair.bam

samtools index /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.vt.bypair.bam