Comments (2)
Hello @mayasheth ,
In the README (https://github.com/edgardomortiz/vcf2phylip) I detail the output formats you can get. However I will specify that the PHYLIP format produced is the "relaxed" version. Honestly I never worked with the package PHYLIP, although they created the PHYLIP format (which is now used by many other phylogenetic programs).
Reading the documentation of Phylip (http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles) I can tell the format my script produces is correct however there is a limitation for the strict Phylip format, the names of the samples must be exactly 10 characters long, you can try renaming your samples and running my script again. I could make my script to truncate the names to 10 characters but this may create non-unique names.
Let me know if this works.
Edgardo
from vcf2phylip.
Please re-open the issue if problem persists, closing this now.
from vcf2phylip.
Related Issues (20)
- 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
- Can't regonized by Treebest to buid NJ tree
- All of the SNPs were removed by vcf2phylip HOT 3
- SNPs that passed the filters: 0 HOT 5
- All SNPs were removed by vcf2phylip HOT 3
- error: unexpected end-of-file. HOT 2
- unexpected token 'newline' error HOT 2
- KeyError: '2': always met this error when converting a vcf file to phylip file. HOT 5
- issues convert vcf file to phylyp HOT 9
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