AdamaJava Wiki
Status: Alpha
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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