Hi all,

I am using freebayes to call variants in diploid organism. So far, my understanding of this program's behavior is as follow:

Assume that there are two SNPs at consecutive nucleotide positions, and there are multiple haplotypes such like:

• haplotype_1: XXXAGXXX
• haplotype_2: XXXTGXXX
• haplotype_3: XXXACXXX

case 1

If haplotype_1 was used as a reference, the variations at the two nucleotide positions are called as two separated SNPs in the output VCF.

 ref   1234   .   A   T ...
 ref   1235   .   G   C ...

case 2

On the other hand, if haplotype_2 was used as a reference, the two variant sites are treated as single MNP in the output VCF.

 ref   1234   .   TG   AC,AG ...

This is, basically, very understandable behavior. However, I sometime like to obtain output always like case 2 even in case 1 because this simplifies some downstream analysis such as investigating amino-acid changes and its genotype.

That is, I want VCF line like below for case 1.

 ref   1234   .   AG   AC,TG ...

Is there any option in freebayes to obtain output like this? or I appreciate if you know any other tool or methodology to get lid of this problem?

Thanks