Lost pairing info after bwa mem

[ArtemLada]

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?

[dpryan]

Try:

 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.

[ArtemLada]

Try:

 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!