Variant using freebayes

Question

[nadiabeg.comsats]

Hi all,

I have 10x genomics data for tetraploid (4n) plant specie. I am using following script for the variant calling.

$free_bayes -f $ref -p 4 $bam >semlo.vcf

I have set ploidy to 4. Is this a correct way of variant calling for tetraploid genomes. In my results I am getting genotype tag (GT:0/0/0/1). So is this correct or something is wrong with vcf calling parameters?

Thanks

Answer 1

[colindaven]

Sounds challenging. Is it really 4n or a double haploid (would be a lot easier).

This thread might be helpful

Tetraploid Snp Calling & Snp Filtering

Make sure you look at your results in a genome browser. Certainly a few read errors in the sequencing might be difficult to discern from the type of variant you just called. Why not just start with 1/1/1/1 and 0/0/1/1 to find something more definitive and less enriched for false positives ?

[nadiabeg.comsats]

Why not just start with 1/1/1/1 and 0/0/1/1 to find something more definitive and less enriched for false positives ? sorry I am not getting your this point. In my results I have SNPs with GT tag :0/1/1/1, few with tag:0/0/0/1, 0/0/0/0, 0/0/1/1. As I am dealing tetraploid specie for the first time. What these tags are exactly defining?

Thanks for the link. I have exactly used the same methodology in my case.