Snp Contig-Synonymous & Nonsynonymous

Question

[jackuser1979]

I am working on non-model organism. I have called SNPs by read mapping illumina reads to reference genome(assembled contigs/scaffolds). I have VCF file with SNP predicted for each contig/scaffold. Recently Ensembl released non-chromosomal genome assembly and also have GTF file(gene prediction based on Ensembl annotation). Now I am trying to find out synonymous and nonsynonymous mutation rate. I find tools that only available for chromosomal level, Is there any script or tool available already for contig level?.

[Zev.Kronenberg]

The VAASST pipeline can annotate variants. All you need is the annotation set in GFF3 format, the reference sequence, the variants, and the lengths of the chromosomes. Converting GTF to GFF3 should also be trivial.

[jackuser1979]

Will this pipeline accept contig lengths?

[Zev.Kronenberg]

Yes the --build flag is a tab delimited file that has 3 columns: 1. seqid/contig_name/scaffold 2. start position (1). 3. length of sequence

Answer 1

[Bioch'Ti]

Hi, You may have also a look to snpEff (SNP effect predictor) which determine the nature (syn/non-syn) of variants. Here is the link: http://snpeff.sourceforge.net/ Hope this helps, C.

[jackuser1979]

I have tried this software. Somehow it doesnot output anything. Did anybody tried running snpEff with VCF as input file containing with contigs instead of chromosomes?

[Lee Katz]

You just have to read the documentation carefully, for adding a genome. It's all there. In terms of contigs or chromosomes... there isn't really a huge difference to snpEff.

[Lee Katz]

This software is really great, and the developer is responsive. The documentation is good too.