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Old 04-17-2017, 05:06 AM   #456
Kristian
Junior Member
 
Location: Europe

Join Date: May 2015
Posts: 8
Default High error rate with BBmap?

Hi Brian,

while trying to call variants on a human MT DNA I noticed the unusually high error rate in mapping with bbmap (37.10 and 36.92 tested) compared to bwa (0.7.12-r1039). Both were run with the default parameters, and below is the output of samtools stats (after sorting and indexing bams). IGV shows many more inverted pairs with bbmap mapping, and this came as a surprise.

I can provide details, however I prefer to share them offline due to the sensitivity of some of the data. Any hints on how to track down the issue?

Many thanks!

BBmap
Code:
BBM: raw total sequences:       537764
BBM: filtered sequences:        0
BBM: sequences: 537764
BBM: is sorted: 1
BBM: 1st fragments:     268882
BBM: last fragments:    268882
BBM: reads mapped:      256366
BBM: reads mapped and paired:   230042  # paired-end technology bit set + both mates mapped
BBM: reads unmapped:    281398
BBM: reads properly paired:     228748  # proper-pair bit set
BBM: reads paired:      537764  # paired-end technology bit set
BBM: reads duplicated:  0       # PCR or optical duplicate bit set
BBM: reads MQ0: 0       # mapped and MQ=0
BBM: reads QC failed:   4282
BBM: non-primary alignments:    0
BBM: total length:      67353071        # ignores clipping
BBM: bases mapped:      32229667        # ignores clipping
BBM: bases mapped (cigar):      29307   # more accurate
BBM: bases trimmed:     0
BBM: bases duplicated:  0
BBM: mismatches:        1672477 # from NM fields
BBM: error rate:        5.706749e+01    # mismatches / bases mapped (cigar)
BBM: average length:    125
BBM: maximum length:    151
BBM: average quality:   30.4
BBM: insert size average:       255.7
BBM: insert size standard deviation:    117.0
BBM: inward oriented pairs:     60121
BBM: outward oriented pairs:    2977
BBM: pairs with other orientation:      48
BBM: pairs on different chromosomes:    0
BWA
Code:
BWA: raw total sequences:       537764
BWA: filtered sequences:        0
BWA: sequences: 537764
BWA: is sorted: 1
BWA: 1st fragments:     268882
BWA: last fragments:    268882
BWA: reads mapped:      266324
BWA: reads mapped and paired:   248064  # paired-end technology bit set + both mates mapped
BWA: reads unmapped:    271440
BWA: reads properly paired:     245908  # proper-pair bit set
BWA: reads paired:      537764  # paired-end technology bit set
BWA: reads duplicated:  0       # PCR or optical duplicate bit set
BWA: reads MQ0: 178     # mapped and MQ=0
BWA: reads QC failed:   0
BWA: non-primary alignments:    0
BWA: total length:      67353071        # ignores clipping
BWA: bases mapped:      33736838        # ignores clipping
BWA: bases mapped (cigar):      32160973        # more accurate
BWA: bases trimmed:     0
BWA: bases duplicated:  0
BWA: mismatches:        603462  # from NM fields
BWA: error rate:        1.876380e-02    # mismatches / bases mapped (cigar)
BWA: average length:    125
BWA: maximum length:    151
BWA: average quality:   30.4
BWA: insert size average:       384.2
BWA: insert size standard deviation:    1040.7
BWA: inward oriented pairs:     67383
BWA: outward oriented pairs:    3645
BWA: pairs with other orientation:      112
BWA: pairs on different chromosomes:    0
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