Variant calling for scaffold genome

Question

[DmissB]

Hey all,

I am working on a triploid non-model organism. We have only a genome at scaffold level (~37k scaffolds, 10k-25k scaffold size, and ~1.8Gbp genome size). Is it possible to perform variant calling on a scaffold genome that is not arranged in chromosomes? Do you have any suggestions for a specific tool to use for this procedure? All I know is GATK

thanks, D.

[Ed]

hello, Have you made any progress on this problem? Recently we meet the same problem. We use GATK to HaplotypeCaller but get into trouble. Thanks.

[samuel.a.odonnell]

Variant calling does not require an assembly to be arranged in chromosomes. What do you see as the issue of using your assembly fo variant calling?

Answer 1

[genomics_buddy]

For variant calling and annotation, u can use snpeff by build your own database with gtf/gff files. It performs for scaffolds or chromosome also if header is matched on all datasets.

Answer 2

[colindaven]

Triploids are very difficult. Most tools are written for diploids.

I think Freebayes is one of the most popular and trustworthy SNP callers which can work on polyploid organisms. Your mileage will vary, but you should be able to find some SNPs at least in areas where the assembly is trustworthy.