DeNovoGear - Detecting denovo SNPs and INDELs in trios using NGS data.

trackavinash · 01-07-2013, 11:37 AM

Hi all,
I'd like to introduce our tool DeNovoGear,

- Denovogear uses a Bayesian approach to detect denovo SNPs and INDELs in trios using NGS data. It calculates a posterior probability for a denovo call by taking into account the genotype likelihoods for each sample at every locus. It gives the user the option to set mutation rate priors according to the data. Separate models have been developed for the autosomes and the X chromosome (based on the sex of the offspring).
- Denovogear also implements a haplotype based phasing algorithm which allows the users to phase denovo mutations to infer the parent of origin for a SNP/INDEL.
- The denovogear model has also been extended to compare paired samples which allows user to call SNP's and INDELs present in only one of the samples. The paired sample model can be used for example to call somatic mutations between tissues, for comparing single cell samples with tissue samples and for comparing tumor/normal pairs.
- Denovogear is designed to be easy to use, users have the option of compiling from source or downloading an executable version of the program. It takes in a BCF file containing the genotype likelihoods generated by samtools as the input. A PED file is required to describe the relationship between the samples. Denovogear includes the option of producing VCF output. More detailed instructions are available in the README.

Project page - https://sourceforge.net/p/denovogear/home/Home/
Comments/Queries contact : aramu at genetics dot wustl dot edu

Feel free to post any questions about the program in this thread, I'll also try to post future updates regarding the program here.
Thanks,
Avinash

akul · 02-27-2013, 02:19 PM

Hi, I have been using your tool and I would like to ask a query about it. I am using it for running paired samples and I am trying to interpret the results in the VCF file-I was taking a look at the REF and ALT tags and there was a case where the REF was C and ALT was T,G,X where the DNM_CONFIG is CT/CC. I was wondering as to how is the ALT as G and X. Thanks

Richard Finney · 01-09-2014, 11:49 AM

Anybody used this ?
Is this any good ?

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01-07-2013, 11:37 AM	#1
trackavinash Member Location: St Louis, USA Join Date: Nov 2011 Posts: 14	DeNovoGear - Detecting denovo SNPs and INDELs in trios using NGS data. Hi all, I'd like to introduce our tool DeNovoGear, - Denovogear uses a Bayesian approach to detect denovo SNPs and INDELs in trios using NGS data. It calculates a posterior probability for a denovo call by taking into account the genotype likelihoods for each sample at every locus. It gives the user the option to set mutation rate priors according to the data. Separate models have been developed for the autosomes and the X chromosome (based on the sex of the offspring). - Denovogear also implements a haplotype based phasing algorithm which allows the users to phase denovo mutations to infer the parent of origin for a SNP/INDEL. - The denovogear model has also been extended to compare paired samples which allows user to call SNP's and INDELs present in only one of the samples. The paired sample model can be used for example to call somatic mutations between tissues, for comparing single cell samples with tissue samples and for comparing tumor/normal pairs. - Denovogear is designed to be easy to use, users have the option of compiling from source or downloading an executable version of the program. It takes in a BCF file containing the genotype likelihoods generated by samtools as the input. A PED file is required to describe the relationship between the samples. Denovogear includes the option of producing VCF output. More detailed instructions are available in the README. Project page - https://sourceforge.net/p/denovogear/home/Home/ Comments/Queries contact : aramu at genetics dot wustl dot edu Feel free to post any questions about the program in this thread, I'll also try to post future updates regarding the program here. Thanks, Avinash

02-27-2013, 02:19 PM	#2
akul Junior Member Location: St.Louis Join Date: Feb 2013 Posts: 2	Hi, I have been using your tool and I would like to ask a query about it. I am using it for running paired samples and I am trying to interpret the results in the VCF file-I was taking a look at the REF and ALT tags and there was a case where the REF was C and ALT was T,G,X where the DNM_CONFIG is CT/CC. I was wondering as to how is the ALT as G and X. Thanks

01-09-2014, 11:49 AM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Anybody used this ? Is this any good ?