MosaikAssembler: No SNPs in gigaBayes GFF when using MOSAIK 1.0.1370

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What steps will reproduce the problem?
1. MosaikAssembler -in sort.dat -ia ref.dat -out res -f gig
2. gigaBayes --gig res.gig --gff res.gff --ploidy diploid --O 2 --debug --
anchor --indel 
3.

What is the expected output? What do you see instead?

gff file(gigaBayes result data) from the gig format result of 
MosaikAssembler-1.0.1370 version has only command line.
and debug data
Screening padded contig position : 10000(10000-10000 unpadded).
Screening padded contig position : 20000(20000-20000 unpadded).
Screening padded contig position : 30000(30000-30000 unpadded).
                             ...

while the gff file from the gig format result of MosaikAssembler-0.9.0891 
version has succeeded.
If we use the gigaBayes, use only older version of mosaik?

What version of the product are you using? On what operating system?

MosaikAssembler-0.9.0891 : success
MosaikAssembler-1.0.1370 : fail
OS : fedora 9 x86_64

Please provide any additional information below.

gigaBayes version : 0.4.1 (Release date : 2008-12-11)

Original issue reported on code.google.com by neolith...@gmail.com on 20 Jan 2010 at 6:21

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This is really strange since MosaikAssembler is virtually unchanged since 
version 0.891.

Since I didn't have the exact files you had, I did the following:

1. Downloaded and unpacked the unified_release_64bit.tar.gz (contains gigaBayes 
0.4.1)
2. Removed the "-inu -uo" options from the MosaikSort line in the RunAnalysis 
script.
3. Removed all of Mosaik* programs from the bin directory and replaced them 
with the
MOSAIK 1.0.1370 binaries
4. Ran the RunAnalysis script.

Performing the above steps, I noticed 11,192 SNP and INDEL calls in the 
GigaBayes gff
file.

One important thing to remember is that the file formats used by MOSAIK changed
between 0.9.0981 and 1.0.1370. Make sure that you redo all of the steps when
comparing the two versions of MOSAIK. 

Could this be the cause?

Cheers,

// Michael

Original comment by snowneb...@gmail.com on 20 Jan 2010 at 10:54

• Changed title: MosaikAssembler: No SNPs in gigaBayes GFF when using MOSAIK 1.0.1370
• Changed state: Started

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Hi,

We no longer maintain gigaBayes. We develop a new genetic-variant detector, 
FreeBayes, instead of gigaBayes.

We'll be glad if you choose FreeBayes as your genetic-variant detector.

FreeBayes: http://bioinformatics.bc.edu/marthlab/FreeBayes

Best,
Wan-Ping

Original comment by WanPing....@gmail.com on 17 Nov 2010 at 7:47

• Changed state: Done