PHYLIP file has not seq text.

Question

[Kagisoralph]

I have a filtered vcf file with 9 wild dog genome samples..i want to run iqtree but when i try to convert my vcf2phylip with the commands

Phython vcf2phylip -i allsamples.vcf -o sample_1.vcf

The output file allsamples.vcf.min.phy has no seq.txt just the sample names..

Less allsamples.vcf.min.phy
~
~
~
~
~
~
~
~
9 0
Sample_1.bam
Sample_2.bam
Sample_3.bam
Sample_4.bam
Sample_5.bam
Sample_6.bam
Sample_7.bam
Sample_8.bam
Sample_9.bam

End...

Please help

Answer 1

[Gio12]

Without much description on what your python script looks like, I can't say what is going wrong. Have you considered using PGDSpider? That should be able to do your conversion.