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  • Lost pairing info after bwa mem

    Dear all,

    Seems I'm missing something trivial, but cant figure out.

    I've got exome seq pipeline. 2 fastq files with corresponding paired reads. Both fastq files contain 92110130 reads each. I am aligning to hg19 as follows:

    bwa mem hg19.fa -t 8 -I R1_001.fastq.gz R2_001.fastq.gz > alignment.sam

    Then converting to BAM:

    samtools view -bS alignment.sam > alignment.bam

    Then checking the statistics:

    samtools flagstat alignment.bam

    Output of last command is:

    92171082 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    91296311 + 0 mapped (99.05%:-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)

    Question: where did all pairing info go?
    Last edited by ArtemLada; 01-10-2016, 01:51 AM.

  • #2
    Try:
    Code:
     bwa mem -t 8 hg19.fa R1_001.fastq.gz R2_001.fastq.gz > alignment.sam
    I imagine that the non-existent "-I" option mucked things up.

    Comment


    • #3
      Originally posted by dpryan View Post
      Try:
      Code:
       bwa mem -t 8 hg19.fa R1_001.fastq.gz R2_001.fastq.gz > alignment.sam
      I imagine that the non-existent "-I" option mucked things up.
      Hey thanks dude! It solved this... Dont know why there was this "-I", probably from obsolete pipeline I was using for older bwa version. Anyway, it worked, fresh look helps a lot!

      Comment

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