the result consists of the character of "RY".

[U201412486]

Hi,
When I run the code below, It produced the result file named "input.min1.phy".
python vcf2phylip.py -i input.vcf
However,the file "input.min1.phy" consists of the character of "RY" which is not the part of DNA nucleotide "AGTC".
Is it normal?
input.zip
sun,

[edgardomortiz]

Hi Sun,

The script was designed for converting VCFs into phylogenetic matrices, these matrices are usually made of several samples and collapse the alleles of a genotype into an ambiguity code. Your VCF only has one sample, and the RY correspond to IUPAC ambiguities, (R = G or A, Y = C or T). In other words, your heterozygous genotypes are now represented by an ambiguity code in the output.

As per another user request (#23) I will add an option so you can get only the ALT nucleotide instead of the heterozygote represented as an ambiguity, but I haven't had time yet to add that code. Is this a feature that you would find useful? or, what kind of output were you expecting?

Edgardo

[U201412486]

Hi Edgardo,
Thank you for your reply.
I expect the output represented by the ambiguity code.However, it can not recognize the condition that the homozygous genotypes in the vcf file which is produced by merging several individual vcf files are represented by the point.
sun

[edgardomortiz]

Would you mind to elaborate? I don't quite get the "represented by the point" part. Also, is this VCF merged from several individuals? I am sure I am misunderstanding something.

[U201412486]

Homozygous genotypes are represented by "0/0" in the vcf format,which means the nucleotides are as same as the reference.However homozygous genotypes are represented by "." after merging multiple VCF files into a single VCF file using vcf-merge software.The vcf file is just like this below.
NC_0009 4411093 . G A 226.50 PASS AC=8;AN=8;BQB=0.786616;DP4=4,0,316,349;DP=778;MQ0F=0;MQ=60;MQB=0.997475;MQSB=1;RPB=0.708333;SF=25,26,27,28;SGB=-0.693147;VDB=0.156993 GT:PL . . . . . . . . . . . . . . . . . . . . . . . . . 1/1:255,255,0 1/1:255,255,0 1/1:255,132,0 1/1:255,255,0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

[edgardomortiz]

The . represents missing genotypes in the VCF format. The genotypes are not modified after the merging, what you are seeing is that not all your samples have the same set of genotypes. Just in case, here is the format specification:
http://samtools.github.io/hts-specs/VCFv4.2.pdf (Page 6)