GATK indel raligner after bfast alignement

david.tamborero · 11-21-2011, 05:30 AM

Hello,

i'm attempting to perform a pipeline to find out somatic mutations of tumor-normal samples sequenced by Illumina paired end reads (100 + 100). After the alignement, I want to do some additional steps (according for instance to http://www.broadinstitute.org/gsa/wi...th_the_GATK_v2), as RemoveDuplicates, Recalibration and Indel_Realignement.

The point is that I want to try the alignement by using bfast, which includes a localign step, in which as far as I know each read is aligned by Smith_Waterman algorithm (allowing gaps) for each CAL. So my question is: when using bfast alignement, is it necessary the GATK_indel_realigner step? I do not know if it is a non wise question, but I want to be sure of performing such GATK step since it's quite demanding and my cluster is not awesome at all.

Thank you for your feedback!

cheers
david

Heisman · 11-21-2011, 06:01 AM

When aligning you will only look at one read at a time, while with IndelRealignment all reads around a predicted indel will be looked at simultaneously. I would go ahead and try both and see what differences you get in your variant calls. If there's say a 1-2% difference, then maybe that wouldn't be enough to care.

david.tamborero · 11-21-2011, 08:23 AM

thank you for your explanation, Heisman.

Then, I guess I have to try it. If the cluster and I are alive to get some results about this issue, I will post them in case anyone more is interested.

Thank you again!
cheers
David

adaptivegenome · 11-21-2011, 09:52 AM

Using the most recent GATK you do not have to do the complete SW realignment if your mapper already produced gapped alignments. See the documentation, there is a shortcut option that saves a little time.

david.tamborero · 11-21-2011, 10:18 AM

I've just seen it, I will try the indel_realignement command of the latest GATK by using the "--consensusDeterminationModel USE_READS" argument, it seems exactly what I was looking for.

Many thanks!

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11-21-2011, 05:30 AM	#1
david.tamborero Member Location: spain Join Date: Feb 2011 Posts: 60	GATK indel raligner after bfast alignement Hello, i'm attempting to perform a pipeline to find out somatic mutations of tumor-normal samples sequenced by Illumina paired end reads (100 + 100). After the alignement, I want to do some additional steps (according for instance to http://www.broadinstitute.org/gsa/wi...th_the_GATK_v2), as RemoveDuplicates, Recalibration and Indel_Realignement. The point is that I want to try the alignement by using bfast, which includes a localign step, in which as far as I know each read is aligned by Smith_Waterman algorithm (allowing gaps) for each CAL. So my question is: when using bfast alignement, is it necessary the GATK_indel_realigner step? I do not know if it is a non wise question, but I want to be sure of performing such GATK step since it's quite demanding and my cluster is not awesome at all. Thank you for your feedback! cheers david

11-21-2011, 06:01 AM	#2
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	When aligning you will only look at one read at a time, while with IndelRealignment all reads around a predicted indel will be looked at simultaneously. I would go ahead and try both and see what differences you get in your variant calls. If there's say a 1-2% difference, then maybe that wouldn't be enough to care.

11-21-2011, 08:23 AM	#3
david.tamborero Member Location: spain Join Date: Feb 2011 Posts: 60	thank you for your explanation, Heisman. Then, I guess I have to try it. If the cluster and I are alive to get some results about this issue, I will post them in case anyone more is interested. Thank you again! cheers David

11-21-2011, 09:52 AM	#4
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	Using the most recent GATK you do not have to do the complete SW realignment if your mapper already produced gapped alignments. See the documentation, there is a shortcut option that saves a little time.

11-21-2011, 10:18 AM	#5
david.tamborero Member Location: spain Join Date: Feb 2011 Posts: 60	I've just seen it, I will try the indel_realignement command of the latest GATK by using the "--consensusDeterminationModel USE_READS" argument, it seems exactly what I was looking for. Many thanks!