SRR1920060 R_2014_03_17_13_28_05_user_P01-233-PPTP_TARGET-40-PPT070-50A-01D TAP_MID0015158.VAR_sA_TARGET-40-PPT070-50A-01D-15 1 NIL blat 33 blat reference.fa query.fa -ooc reference.ooc -minIdentity=90 tmp.psl 2 1 cross_match 1.080812 cross_match query.fa amplicon.fa -minscore 30 -masklevel 20 -raw -discrep_lists > .crossmatch 3 2 crossmatch2SAM 1.0 crossmach2SAM -i .crossmatch -o .sam 4 3 samtools 0.1.8 samtools view -Sb .sam > .bam 5 4 picard 1.86 java -jar SortSam.jar I=.bam O=sorted.bam SORT_ORDER=coordinate 6 5 picard 1.86 java -jar AddOrReplaceReadGroups.jar I=.sorted.bam O=.sorted.rg.bam RGLB=LIBRARY RGPL="Ion Torrent" RGPU=RUN RGSM=SAMPLE RGCN=BCM