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One thing to keep in mind when you treat them as unpaired, is that your coverage doubles. That could make the difference.
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Originally posted by dpryan View PostJust look at the output BAM in IGV.
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bwa mem with paired/unpaired reads
I have a quick question for all bwa mem users (or author, if you have time Heng).
I have some reads from a simulated exome study that have been modified to have a 50/50 allele balance with one allele having a 3 bp deletion at a particular locus. The reads that cover this locus are paired, and so I have a set of reads:
reads.f.fq, and reads.r.fq
If I align using the paired reads:
bwa mem ref.fa reads.f.fq reads.r.fq ...
and process the results with samtools mpileup, no variant is found.
However, if I concatenate the read files together, and align without pairing:
cat reads.f.fq reads.r.fq > reads.fq
bwa mem ref.fa reads.fq ...
the variant is discovered as expected.
Just in case I had the orientation of the reverse reads incorrect, I tried the first command with the reverse complement of the read.r.fq file, without success.
Is there any bwa mem output I should look for that would indicate improper mate-pairing or other invalid input?
thanks,
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