vcf2phylip

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output for phased data

5

Hi there, Thank you for making this super useful tool! Issue #23 was a really helpful improvement for utilizing heterozygous sites. I was wondering if it would be feasible to...

erikenbody

error: unexpected end-of-file.

2

I ran vcf2phylip to generate the phylip file and got an error: `error: unexpected end-of-file.` After checking the .phy file and found the length of name + padding is not...

zhujack8

SNPs that passed the filters: 0

5

Hello, when I tried to convert VCF format( [Uploading timetree_1.vcf.gz…]() ) to Phylip format using vcf2phylip, all the SNPs was not preserved. This data is 9 samples extracted from a...

Peijiawei2022

I converted vcf file to fasta file, then I used **_Treebest_** to build NJ tree with command " treebest nj -W -t ntmm -b 1000 fastfile > result", Error occurred:...

Sherry520

error

1

File "/Users/awaisrasheed/vcf2phylip.py", line 71 vcf2phylip/vcf2phylip.py at master · edgardomortiz/vcf2phylip · GitHub ^ SyntaxError: invalid character '·' (U+00B7)

awaisrasheedqau

output path issue

6

How to set a certain output path for the PHY? My VCF is too large and my C drive is too small to hold the output PHY. Thanks.

CHAOS324

Deciding an outgroup to root the tree

1

Hi there, I am not sure which sample I use an outgroup to root the tree. Is there any way to choose midpoint while converting a vcf file to phlylip...

Ram-Nagar

KeyError: '2': always met this error when converting a vcf file to phylip file.

3

I have modified the variety names to be four digits, such as 4111, ensuring they are within 10 characters. However, I am still encountering this error. Could you please teach...

mxtu97