Comments (5)
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
from vcf2phylip.
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
from vcf2phylip.
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.
from vcf2phylip.
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
from vcf2phylip.
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)
from vcf2phylip.
Related Issues (20)
- Outputfile(.phy) couldn't be open by Phylip and FastTree HOT 3
- input file can't be file.vcf.gz? HOT 3
- Error from vcf2phylip v2.3 when converting GATK vcf HOT 8
- Phylogenetic tree HOT 6
- output for phased data HOT 5
- Multiple VCF files? HOT 7
- Hours taken to find the ploidy HOT 9
- Give option for name and directory of output file HOT 3
- Installation problem HOT 3
- transfer vcf file of SV into phylip failed HOT 5
- Invalid character * in the alignment HOT 10
- Coordinates of alignment sites HOT 2
- UnboundLocalError: local variable 'used_sites' referenced before assignment HOT 3
- Max character length for seq IDs HOT 2
- Deciding an outgroup to root the tree HOT 1
- output path issue HOT 6
- error HOT 1
- ImportError: No module named pathlib HOT 2
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from vcf2phylip.