Pls help with noobish format conversion question.

[Humble Simpleton]

I need to know how I can convert personal genome SNP format (pgSnp) to bam/bai and to fastq, and vice versa. The only tools relevant to pgSnp on galaxy convert VCF and CG mastervar to pgSNP. If anyone can help with the above, that would be awesome. Thanks in advance.

[Humble Simpleton]

BUMP! Anyone?

I've stumbled upon this program which I think might be relevant to what I'm trying to do. Let me know if anyone has any input:

GenomeGems performs simple comparisons using graphs and tables of data produced from different samples, and a wide and detailed visualization of the Deep Sequencing pre-processed data. GenomeGems integrates well with the University of California Santa Cruz (UCSC) Genome Browser for the purpose of SNP visualization within investigated chromosomes. This function is made possible by development of algorithms for conversion of a pre-processed input data to a Personal Genome SNP data format (PgSNP) , which can be viewed and further analyzed using UCSC . In addition to all of this, GenomeGems suggests a few useful external databases for further SNP investigation.

http://www.tau.ac.il/~nshomron/GenomeGems/Manual.html

Thanks in advance.

[arolfe]

doesn't look like you can

pgSnp looks like it just contains information on SNPs; it's what you might get after aligning a fasta or fastq file of sequencing reads to produce a BAM file and then analyzing the BAM file with a tool like freebayes or mpileup to find differences between your sequencing reads and the reference sequence. You can't go back from pgSnp to the other formats because it's a summary of them. You need to find the original datafiles that were used to generate your pgSnp files.

[Humble Simpleton]

pgSnp looks like it just contains information on SNPs; it's what you might get after aligning a fasta or fastq file of sequencing reads to produce a BAM file and then analyzing the BAM file with a tool like freebayes or mpileup to find differences between your sequencing reads and the reference sequence. You can't go back from pgSnp to the other formats because it's a summary of them. You need to find the original datafiles that were used to generate your pgSnp files.

Thanks for the input! Do you have any advice on getting BAM and fastq > pgSnp?

[Humble Simpleton]

BUMP! Anyone with any input on getting BAM and/or fastq into pgSnp? Thanks!

[Humble Simpleton]

Okay, I haven't had any luck getting the SEQ answers that I need. I will pay someone if they can tell me how to get fastq and bam to pgSnp in such a way that I can reproduce the process as needed. Let me know if anyone is interested. Thanks.