*.tags.tsv to bam file? SNPs to VCF?

[Angélica Cuevas]

Hello,

I just have a few questions about exporting the output files of stacks into a more generic format: 

1. using ustacks I created *.tags.tsv files. Taking into account that even though I run a denovo I have information of the coordinates (to a closely related species genome) of each loci formed in the *.tags.tsv file, can I somehow generate bam files from these denovo formed *.tags.tsv files?

2. Does the Locus ID in the *.tags.tsv file matches the one in the catalog?

3. is the information in *.snps.tsv those polymorphism found when mapping to the catalog? because I have a *.snps.tsv file per individual, it make me think that those are the SNPs found when mapping against the catalog? However eat position of the locus is reported whether it varies or not regarding the catalog consensus.

4. If I use the utility in "populations" to export a *.vcf file, does this vcf is per individual?, I assume the *.vcf would contain only those SNPs founds when comparing each individual tag to the catalog, right?

Thanks a lot in advance for your help!

best,

Angelica

[Nicolas Rochette]

Hi Angelica,

1. It is hard to answer without knowing what the end purpose is. It should be possible, but may not be what you want. I would recommend not transforming and reusing the information in the internal Stacks files unless you are sure you understand the operations that Stacks performs internally.

2. No. There are two types of "locus IDs": the sample locus IDs (for sample-specific loci, that's what you'll find in sample files) and the catalog locus IDs (for catalog loci). The matches files give the correspondence.

3. These files are the result of the search for heterozygous loci within each individual.

4. VCF is a (standard) format that lists known polymorphisms and the associated genotypes. You should try it out and look at the contents of the file.

Best,

Nicolas

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Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Angélica Cuevas]

Hi Nicolas,

Thanks a lot for the answers.

What I'm trying to do is to put coordinates in the loci (and its reads) from the denovo. I can generate coordinates (from a closely related species genome) to the catalog and with that information I would like to generate *.bam files from the denovo with the coordinates to use later in a downstream pipe line. 

I just think mapping to a related species could be biasing the data (picking up reads that are more similar to that specific species and throwing reads that might actually give polymorphic information), it might be a better approach to generate a denovo with the rad data and later put coordinates on it, and the reason why I want to put coordinates on those denovo loci is that I need a ref genome from a downstream pipeline.

Finally about the vcf, I was just wondering where those SNPs come from, from mapping each individual against the catalog I assume, right? or does it use SNPs between populations?

Thanks again!

best,

Angelica

[Julian Catchen]

Hi Angelica,

See the recent paper in Methods in Ecology and Evolution for a
description of how to do what you are proposing (align denovo assembled
consensus sequences against closely-related genome):

http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12775/abstract

(Stacks supports this and has scripts to integrate the coordinates.)

For your question on the SNP calling, see the 2013 or 2011 Stacks papers.

Best,

julian

>> 4. If I use the utility in "/populations/" to export a *.vcf file,

[Angélica Cuevas]

Thanks Julian!