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Old 01-10-2016, 01:44 AM   #1
ArtemLada
Junior Member
 
Location: Davis

Join Date: Oct 2010
Posts: 3
Default 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.
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Old 01-10-2016, 03:02 AM   #2
dpryan
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Location: Freiburg, Germany

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Default

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.
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Old 01-10-2016, 10:26 PM   #3
ArtemLada
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Location: Davis

Join Date: Oct 2010
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Default

Quote:
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!
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bam, bwa mem, exome sequecing, paired, samtools flagstat

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