Hi Alec, Yes, somehow I also found this right after I sent out the email.... So if I want to filter this kind of alignment out, is there a flag could use?
I am still wondering the big difference between mapped reads count? btw, the 'supplimentary' word in flagstat output, is a typo? Thanks for response. Daofeng On Wed, Oct 29, 2014 at 10:55 AM, Alec Wysoker <al...@broadinstitute.org> wrote: > 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 > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Samtools-help mailing > listSamtools-help@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/samtools-help > > >
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