Lost pairing info after bwa mem

ArtemLada · 01-10-2016, 01:44 AM

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 · 01-10-2016, 03:02 AM

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.

ArtemLada · 01-10-2016, 10:26 PM

Quote:

Originally Posted by dpryan

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!

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01-10-2016, 01:44 AM	#1
ArtemLada Junior Member Location: Davis Join Date: Oct 2010 Posts: 3	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 at 01:51 AM.

01-10-2016, 03:02 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.