BAM output

The output of splitcode can be in the form of BAM files (Li, Handsaker, et al., Bioinformatics 2009). These unaligned BAM files are convenient for storing the output sequences along with the metadata associated with tag identification.

To output a BAM file, run splitcode with the --out-bam option, along with options such as --com-names, --seq-names, --loc-names, and --bc-names.

An example BAM output (as viewed with samtools), would look like:

read1  12      *       0       0       *       *       0       0       CCCCCCCCCGGGCCCCCCCCCGGGAACCTAG KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK CB:Z:CCCCCCCGGCCCCCCCGG BI:i:0  BC:Z:AAAAAAAAAAAAAAAA   LX:Z:tag1:0,0-7,tag2:0,9-11,tag1:0,12-19,tag2:0,21-23
read2  12      *       0       0       *       *       0       0       CCCCCCCCCGGGCCCCCCCCCGGGAACCTAG KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK CB:Z:CCCCCCCGGCCCCCCCGG BI:i:0  BC:Z:AAAAAAAAAAAAAAAA   LX:Z:tag1:0,0-7,tag2:0,9-11,tag1:0,12-19,tag2:0,21-23