PubMed: VarScan: Variant detection in massively parallel sequencing of individual and

Newsbot! · 06-23-2009, 05:00 AM

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Related Articles VarScan: Variant detection in massively parallel sequencing of individual and pooled samples.

Bioinformatics. 2009 Jun 19;

Authors: Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L

SUMMARY: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprece-dented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains chal-lenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read align-ers. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples. Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics, implemented as a Perl package and supported on Linux/UNIX, MS Windows, and Mac OSX. CONTACT: dkoboldt@genome.wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 19542151 [PubMed - as supplied by publisher]

More...

MQ-BCBB · 09-23-2009, 12:53 PM

Hello,
The program looked very useful from the description in the paper. I tried installing in Mac and Linux but it gave me errors (needed Math::Pari). I googled it and found some information but have not yet been able to solve the issue. Any tips?

Thank you!

zhangmj · 10-21-2009, 04:39 PM

http://search.cpan.org/~ilyaz/Math-P...010801/Pari.pm ，install it。

MQ-BCBB · 10-21-2009, 04:44 PM

Thank you!
Shortly after I posted, I figure it out. The program worked fine. In fact, when I used ssaha2+samtools pileup or BLAT+Varscan, I obtained similar results in the number of SNPs that were known.

bioenvisage · 12-01-2009, 06:19 AM

I made alignments with bowtie and when i run varscan iam getting the error as alignment format not recognised, can some bdy help me ...

Lien · 04-29-2010, 10:49 PM

Hi,

I'm trying to use Varscan to call indels.
I started from a pileup file made with Samtools, after alignment with Bowtie. When I used Varscan to call SNPS, it worked fine, but now it doesn't seem to find any indels. Should I change something in the parameters? Or do I need to change parameters during the alignment with Bowtie (I used all default parameters).
I really don't understand why it can call SNPs, but not indels.

nilshomer · 04-29-2010, 11:14 PM

Quote:

Originally Posted by Lien

Hi,

I'm trying to use Varscan to call indels.
I started from a pileup file made with Samtools, after alignment with Bowtie. When I used Varscan to call SNPS, it worked fine, but now it doesn't seem to find any indels. Should I change something in the parameters? Or do I need to change parameters during the alignment with Bowtie (I used all default parameters).
I really don't understand why it can call SNPs, but not indels.

Bowtie does not support indels. Try BFAST or BWA, which support indels.

waseem · 06-17-2011, 08:16 AM

Can we use topHat for the similar problem?

waseem · 07-21-2011, 07:41 AM

Now I am trying to use bfast with BWA to map our reads. for bfast+bwa workflow, there are total five steps:
1. The first step is to create a reference genome from an input FASTA file that contains all
the sequence to which we wish to align. (bfast fasta2brg)
2. The second step is to create indexes of the reference genome, which was created in the
first step. (bfast index)
3. The third step is to find candidate alignment locations (CALs) for each read. (bfast match)
4. The fourth step is to fully align each CAL for each read. (bfast localalign)
5. The fifth and final step is to prioritize the final alignments. (bfast postprocess)

Now I got the problem in step 4. Aborted error came out. Based on my search, I guess our origninal paired reads is too large for this software. Now I try to break the one end reads into several parts, then repeat the first three steps in bfast.
Any Guidance??
Best,

nilshomer · 07-21-2011, 07:42 AM

What is the error message in step 4 (copy and paste please). Can you isolate it to just a few reads for ease of debugging?

Flor · 08-07-2011, 11:41 PM

Hi,
Probably a very stupid newbie question, but a have a problem with the pileup2indel option of Varscan. When I look in Samtools tviewer I find several Indels with a varfreq of 100%, however Varscan gives these variants a Varfreq of 50%. The problem seems to be that varscan takes the coverage of the base before the indel as reads1, thereby approximately doubling the total number of reads on the indel position. This results in varfreqs of about half the real variant frequency.....What am I doing wrong???

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06-23-2009, 05:00 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,397	PubMed: VarScan: Variant detection in massively parallel sequencing of individual and Syndicated from PubMed RSS Feeds Related Articles VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Jun 19; Authors: Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L SUMMARY: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprece-dented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains chal-lenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read align-ers. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples. Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics, implemented as a Perl package and supported on Linux/UNIX, MS Windows, and Mac OSX. CONTACT: dkoboldt@genome.wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 19542151 [PubMed - as supplied by publisher] More...

12-01-2009, 06:19 AM	#5
bioenvisage Member Location: it Join Date: Oct 2009 Posts: 40	I made alignments with bowtie and when i run varscan iam getting the error as alignment format not recognised, can some bdy help me ... Last edited by bioenvisage; 12-01-2009 at 07:17 AM.

06-17-2011, 08:16 AM	#8
waseem Member Location: Urbana Join Date: May 2011 Posts: 11	VarScan indels problem Can we use topHat for the similar problem?

09-23-2009, 12:53 PM	#2
MQ-BCBB Member Location: Maryland Join Date: May 2009 Posts: 22	Hello, The program looked very useful from the description in the paper. I tried installing in Mac and Linux but it gave me errors (needed Math::Pari). I googled it and found some information but have not yet been able to solve the issue. Any tips? Thank you!

10-21-2009, 04:39 PM	#3
zhangmj Junior Member Location: chin Join Date: Aug 2008 Posts: 4	http://search.cpan.org/~ilyaz/Math-P...010801/Pari.pm ，install it。

10-21-2009, 04:44 PM	#4
MQ-BCBB Member Location: Maryland Join Date: May 2009 Posts: 22	Thank you! Shortly after I posted, I figure it out. The program worked fine. In fact, when I used ssaha2+samtools pileup or BLAT+Varscan, I obtained similar results in the number of SNPs that were known.

04-29-2010, 10:49 PM	#6
Lien Member Location: Leuven Join Date: Dec 2009 Posts: 34	Hi, I'm trying to use Varscan to call indels. I started from a pileup file made with Samtools, after alignment with Bowtie. When I used Varscan to call SNPS, it worked fine, but now it doesn't seem to find any indels. Should I change something in the parameters? Or do I need to change parameters during the alignment with Bowtie (I used all default parameters). I really don't understand why it can call SNPs, but not indels.

07-21-2011, 07:41 AM	#9
waseem Member Location: Urbana Join Date: May 2011 Posts: 11	Now I am trying to use bfast with BWA to map our reads. for bfast+bwa workflow, there are total five steps: 1. The first step is to create a reference genome from an input FASTA file that contains all the sequence to which we wish to align. (bfast fasta2brg) 2. The second step is to create indexes of the reference genome, which was created in the first step. (bfast index) 3. The third step is to find candidate alignment locations (CALs) for each read. (bfast match) 4. The fourth step is to fully align each CAL for each read. (bfast localalign) 5. The fifth and final step is to prioritize the final alignments. (bfast postprocess) Now I got the problem in step 4. Aborted error came out. Based on my search, I guess our origninal paired reads is too large for this software. Now I try to break the one end reads into several parts, then repeat the first three steps in bfast. Any Guidance?? Best,

07-21-2011, 07:42 AM	#10
nilshomer Super Moderator Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,279	What is the error message in step 4 (copy and paste please). Can you isolate it to just a few reads for ease of debugging?

08-07-2011, 11:41 PM	#11
Flor Junior Member Location: Netherlands Join Date: Nov 2010 Posts: 1	Hi, Probably a very stupid newbie question, but a have a problem with the pileup2indel option of Varscan. When I look in Samtools tviewer I find several Indels with a varfreq of 100%, however Varscan gives these variants a Varfreq of 50%. The problem seems to be that varscan takes the coverage of the base before the indel as reads1, thereby approximately doubling the total number of reads on the indel position. This results in varfreqs of about half the real variant frequency.....What am I doing wrong???