Man pages for compbiocore/qckitalign
Quality Control for Mapped Reads
| bam_reads | Returns the number of distinct reads in the BAM file... |
| bam_records | Returns the number of alignment records in the BAM file... |
| chimeric_proportion | Returns proportion of reads that have been mapped to two... |
| chimeric_reads | Identifies reads by index record that have been mapped to two... |
| chimeric_rname | Identifies reads with the same qname but different rname from... |
| chimeric_tags | Identifies reads with the SA tag, indicating a chimeric read... |
| chromosome | chromosome |
| cigar_partition | cigar partitioning |
| cigar_prof | cigar profile |
| cover_age | coverage rate: mean, median and sd |
| insert_size | Insert size |
| map_qua | mapping quality |
| mult_map | multiple mapping |
| num_chimeric | Return number of chimeric reads from a bamfile. |
| unmapped_reads | return name of unmapped reads |
| unq_map | unique mapping |
