Question: How Do You Do Local Realignment Around Indels For Exome Sequencing?
gravatar for Travis
9.6 years ago by
Travis2.8k wrote:

Hi all,

I am wondering how people generally go about local realignment around indels in their workflow?

The most popular programs seem to be SRMA and GATK - does anyone use anything else?

In my initial tests this seems to be a VERY time-consuming step when compared to the initial alignment step. Does anyone employ methods of speeding up the process? For example, only realigning within exonic coordinates OR perhaps performing variant calling first and then using the coordinates from the VCF to restrict the areas where realignment is performed?

I am trying to set up a SNP/Indel workflow and realignment seems to slow it to the the point where it becomes useless for anything but small numbers of samples. I tested on a single chromosome and it took 4.5 hours. Alignment and variant calling without realignment only took about 1.5 hours for the whole genome!

Thanks in advance!

ADD COMMENTlink modified 9.6 years ago by Docroberson300 • written 9.6 years ago by Travis2.8k

Did you find anything new in past months? I am now facing similiar situation as you were, considering which tool (if any) to use. Thanks.

ADD REPLYlink modified 8.3 years ago • written 8.3 years ago by Biomonika (Noolean)3.1k
gravatar for Drio
9.6 years ago by
United States
Drio920 wrote:

Take a look to this question and my answer (and the comments). SRMA allows realignment of specific regions. That will help you reduce the runtime of the process.

ADD COMMENTlink modified 16 months ago by _r_am32k • written 9.6 years ago by Drio920

I remember the question - I asked it :) My question here is a more general one.

ADD REPLYlink written 9.6 years ago by Travis2.8k
gravatar for Docroberson
9.6 years ago by
the lab
Docroberson300 wrote:

I typically use BWA for alignments to get indels at the same time. Pretty fast (on par with bowtie). Alternatively I've used NOVOALIGN to do alignment and indel calculations in one step also. Very good at finding both substitutions and indels, but VERY slow and resource intensive compared to other software.

ADD COMMENTlink written 9.6 years ago by Docroberson300

I am more curious about the local realignment step that occurs post BWA etc.

ADD REPLYlink written 9.6 years ago by Travis2.8k
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