Question: Large Deletions With Bwa And Single End Reads
2
gravatar for Travis
8.6 years ago by
Travis2.8k
USA
Travis2.8k wrote:

Hi,

I am trying to detect deletions approximately 66bp in length by mapping 90 base reads to the human genome with BWA (and using GATK). By fine tuning the alignment parameters I have managed to increase my maximum detected indel length to around 30 bases but so far I have been unable to improve on that. I have increased the maximum number of gap extensions to 200 and reduced the gap extension penalty to zero so in my head at least, I thought the larger indels would be detectable. Can anyone offer any insight?

Thanks in advance.

ADD COMMENTlink modified 8.3 years ago by Ying W4.0k • written 8.6 years ago by Travis2.8k
1

You might consider artificially splitting your read into two fragments in various lengths and mapping them separately? Tophat uses that strategy for transcript splicing.

ADD REPLYlink written 8.6 years ago by Damian Kao15k

Hi @Travis, are you trying to find deletions in the reference that are insertions in your sequencing sample, or deletions in your sample that are insertions in the reference, and split your reads into halves?

ADD REPLYlink written 8.6 years ago by 2184687-1231-83-5.0k

At the minute I am trying to find two deletions in the 60-66bp range. The deletion is in the reads, not the reference.

ADD REPLYlink written 8.6 years ago by Travis2.8k

I have detected deletions in the 45-64b range using bwa/gatk (100bp PE Illumina), but haven't had them validated so.. I don't want to say much more than that. I was under the impression from recent conference talks that identification of deletions over 30bp (1/3rd read length) wasn't likely to happen with this particular toolchain.

ADD REPLYlink written 8.6 years ago by Daniel Swan13k

Cheers Daniel. I am attempting to tweak another parameter or two so will see what happens on that front and update. I am determined to do it somehow!

ADD REPLYlink written 8.6 years ago by Travis2.8k

Good advice, but I am specifically attempting to address the program without customization of anything other than existing program parameters.

ADD REPLYlink written 8.6 years ago by Travis2.8k

You could also try other aligners such as blat, gsnap, and bfast.

ADD REPLYlink written 8.6 years ago by Sean Davis26k

Bfast will be my next port of call if I can't get the desired resuls from bwa. I spotted Nils commenting somewhere about the fact that his tests showed better indel detecting abilities than with bwa. The only drawback is speed.

ADD REPLYlink written 8.6 years ago by Travis2.8k

Bfast will be my next port of call if I can't get the desired results from bwa. I spotted Nils commenting somewhere about the fact that his tests showed better indel detecting abilities than with bwa. The only drawback is speed.

ADD REPLYlink written 8.6 years ago by Travis2.8k

Does anyone know what is limiting BWA's ability to find a 63bp deletion when it can find a 30bp deletion without a problem? Gap extension penalties are turned off.

ADD REPLYlink written 8.6 years ago by Travis2.8k
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