-C Append append FASTA/Q comment to SAM output.
This option can be used to transfer read meta information (e.g. barcode) to the SAM output.
Note that the FASTA/Q comment (the string after a space in the header line) must conform the
SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
This is useful when cell barcode information (CB tag) was added to the FASTQ read names in the comment part (read name + space + SAM tags separated by TABs):
Add option to add FASTQ comment to SAM output.
For example BWA supports this with the
-C
option:This is useful when cell barcode information (
CB
tag) was added to the FASTQ read names in the comment part (read name + space + SAM tags separated by TABs):