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  • bwa outputs bam with less reads than in input fastq

    I downloaded a publicly available bam file and ran samtools flagstat on it. The output is here:

    482805326 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    235328156 + 0 mapped (48.74%:nan%)
    482805326 + 0 paired in sequencing
    241402663 + 0 read1
    241402663 + 0 read2
    235328156 + 0 properly paired (48.74%:nan%)
    235328156 + 0 with itself and mate mapped
    0 + 0 singletons (0.00%:nan%)
    0 + 0 with mate mapped to a different chr
    0 + 0 with mate mapped to a different chr (mapQ>=5)

    Next, I extracted reads from the bam into two fasta files. The sum of reads in both was 482805326, so equal as in the bam. I aligned the fastq files again (bwa aln and bwa sampe), and ran samtools flagstat on the resulting bam. Here is the output:

    387280125 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    387280125 + 0 mapped (100.00%:nan%)
    387280125 + 0 paired in sequencing
    194031131 + 0 read1
    193248994 + 0 read2
    375578347 + 0 properly paired (96.98%:nan%)
    381759377 + 0 with itself and mate mapped
    5520748 + 0 singletons (1.43%:nan%)
    5108005 + 0 with mate mapped to a different chr
    4124551 + 0 with mate mapped to a different chr (mapQ>=5)

    And what I don't understand is where is almost 100M reads gone? I haven't found any information on bwa removing unmapped/bad quality/duplicate reads, so I am wondering. Any hints?

    I am using bwa 0.5.9-r16
    Last edited by seru; 03-06-2012, 03:07 AM. Reason: added tool version

  • #2
    Same here

    I have this same problem. Did you ever figure out how to fix it?

    Update: The missing reads in the bam file were due to the following error:
    [bwa_sai2sam_pe_core] print alignments... [E::sam_parse1] CIGAR and query sequence are of different length
    [W::sam_read1] parse error at line 11261615
    [main_samview] truncated file.

    All of this happened after I switched to a new reference genome (mm10). I'm not getting the error with mm9. I don't have a good explanation but I think that the version of mm10 I tried to use must have been somehow corrupted.
    Last edited by petervangalen; 11-05-2016, 03:37 AM.

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    • #3
      Note the "100%" mapped metric, which means that the unmapped reads were excluded from the output.

      Comment

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