qMule BamMismatchCounts

This qMule mode provides, for reads that mapped full-length, a breakdown of how many mismatches are in each read. It also logs a breakdown of reads that were in the BAM but not included in the mismatch tally so they were unmapped or had a CIGAR string indicating insertion (I), deletion (D), padding (P), skipping (N), or clipping (S,H).

qmule org.qcmg.qmule.BamMismatchCounts <bam/sam filename> <output filename>

The mismatch tally output looks like this:

mismatch    reads_number    ratio_to_(fullmapped,total)
0   805075  (83%,80%)
1   109567  (11%,10%)
2   22495   (2%,2%)
3   8918    (0%,0%)
4   5763    (0%,0%)
5   4773    (0%,0%)
6   776 (0%,0%)
7   622 (0%,0%)
8   518 (0%,0%)
9   367 (0%,0%)
10  301 (0%,0%)
11  256 (0%,0%)
12  179 (0%,0%)
13  156 (0%,0%)
14  127 (0%,0%)
…

It automatically creates a log file named <output filename="">.log. It extracts below shows a example breakdown of the reads in the BAM. Of the 999912 reads, 960361 were mapped full-length and so were used to create the mismatch tally.

20:04:42.378 [main] INFO org.qcmg.qmule.BamMismatchCounts - total records in file: 999912
20:04:42.378 [main] INFO org.qcmg.qmule.BamMismatchCounts - unmapped records: 6874
20:04:42.379 [main] INFO org.qcmg.qmule.BamMismatchCounts - records with clipping (CIGAR S,H): 13150
20:04:42.379 [main] INFO org.qcmg.qmule.BamMismatchCounts - records with indel (CIGAR I,D): 19527
20:04:42.379 [main] INFO org.qcmg.qmule.BamMismatchCounts - records with skipping or padding (CIGAR N,P): 0
20:04:42.379 [main] INFO org.qcmg.qmule.BamMismatchCounts - records mapped full-length: 960361
20:04:42.380 [main] INFO org.qcmg.qmule.BamMismatchCounts - records mapped full-length but missing MD field: 0