Hi Daofeng,
bwa mem produces supplementary reads. A supplementary read is an
additional alignment for the same read. Note that:
33187055 (total BWA MEM records) - 18543 (supplementary alignments) ==
33168512 (total BWA ALN records)
-Alec
On 10/29/14, 11:47 AM, Daofeng Li wrote:
Dear BWA lists,
Recently I tried to use BWA mem algorithm for aligning our reads and I
found there is some difference between their results.
So I have 75bp single end reads, I have reads file from 4 lanes and I
did alignment separately and merged later, below are samtools flagstat
output for aln and mem, respectively:
mem:
samtools flagstat combine_index1.bam
33187055 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
18543 + 0 supplimentary
0 + 0 duplicates
28739571 + 0 mapped (86.60%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
aln:
$ samtools flagstat combine_index1.bam
33168512 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplimentary
0 + 0 duplicates
22191474 + 0 mapped (66.91%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
my question is that why the total reads number would differ? And also
there is large difference between mapped reads count also... is this
normal?
tools versions:
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.10-r789
Program: samtools (Tools for alignments in the SAM format)
Version: 1.1 (using htslib 1.1)
Thanks.
Daofeng
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