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edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GNU General Public License v3.0
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all SNPs were removed when converting my vcf file by using vcf2phylip #10

Closed yiranzou12138 closed 5 years ago

yiranzou12138 commented 5 years ago

Hello,

I found that all my SNPs were removed after converting my vcf file. I did that on the Linux system, the command I type is "python vcf2phylip.py -m 0 -fi 1111.filter.vcf".
And the result is "Number of samples in VCF: 8 Total of genotypes processed: 130883 Genotypes excluded because they exceeded the amount of missing data allowed: 130883 Genotypes that passed missing data filter but were excluded for not being SNPs: 0 SNPs that passed the filters: 0"

I don't know why all my SNPs were removed, and how can I fix that problem?

Appreciate for your help! ^_^

edgardomortiz commented 5 years ago

Hi, I just ran a test with one of my files: vcf2phylip.py -i file.vcf -m 0 And ran without errors, which tells me that there must be something in your vcf that is not standard. Would you mind emailing me a few thousand lines to find out the problem?

yiranzou12138 commented 5 years ago

Hi, I just ran a test with one of my files: vcf2phylip.py -i file.vcf -m 0 And ran without errors, which tells me that there must be something in your vcf that is not standard. Would you mind emailing me a few thousand lines to find out the problem?

Hi Edgardo, I have emailed my file to you. Really appreciate for your help.

edgardomortiz commented 5 years ago

Hi Zoey,

Thanks for finding this bug, it was not a problem with your file but with my code. Please re-clone the repository and try again, it should be fixed. Also, just to be sure, repeat a few of your other files to verify you get the same results as before.

Edgardo

yiranzou12138 commented 5 years ago

Hi Zoey,

Thanks for finding this bug, it was not a problem with your file but with my code. Please re-clone the repository and try again, it should be fixed. Also, just to be sure, repeat a few of your other files to verify you get the same results as before.

Edgardo

Hi Edgardo,

Thanks for your help. It works now. I have tried other files and they showed the same result as before. ^_^ Zoey