edgardomortiz vcf2phylip issues

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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issues

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Default output type of vcf2phylip.py: too many ambiguous nucleotide sequences?

#51 LiuCanidk opened 1 month ago
7
issues convert vcf file to phylyp

#50 lophostoma opened 5 months ago
9
KeyError: '2': always met this error when converting a vcf file to phylip file.

#49 mxtu97 closed 6 months ago
5
unexpected token 'newline' error

#48 faulk-lab closed 6 months ago
2
error: unexpected end-of-file.

#47 zhujack8 opened 10 months ago
2
All SNPs were removed by vcf2phylip

#46 paul1000ton-coder closed 11 months ago
3
SNPs that passed the filters: 0

#45 Peijiawei2022 closed 1 month ago
5
All of the SNPs were removed by vcf2phylip

#44 bjarnebartlett closed 9 months ago
3
Can't regonized by Treebest to buid NJ tree

#43 Sherry520 opened 1 year ago
0
ImportError: No module named pathlib

#42 lyn320 closed 1 year ago
2
error

#41 awaisrasheedqau opened 1 year ago
1
output path issue

#40 CHAOS324 opened 1 year ago
6
Deciding an outgroup to root the tree

#39 Ram-Nagar opened 2 years ago
1
Max character length for seq IDs

#38 Neato-Nick closed 3 years ago
2
UnboundLocalError: local variable 'used_sites' referenced before assignment

#37 danielyao12 closed 3 years ago
3
Coordinates of alignment sites

#36 matthewglasenapp closed 3 years ago
2
Invalid character * in the alignment

#35 Rahmmy closed 3 years ago
10
transfer vcf file of SV into phylip failed

#34 QianghuiZhu closed 3 years ago
9
Installation problem

#33 XK4959 closed 3 years ago
3
Give option for name and directory of output file

#32 vmkalbskopf closed 3 years ago
3
Hours taken to find the ploidy

#31 vmkalbskopf closed 3 years ago
9
Multiple VCF files?

#30 TakashiKoyama closed 3 years ago
7
output for phased data

#29 erikenbody opened 3 years ago
5
Phylogenetic tree

#28 devenderarora closed 3 years ago
6
Error from vcf2phylip v2.3 when converting GATK vcf

#27 seanimal closed 4 years ago
8
input file can't be file.vcf.gz?

#26 yanzhongsino closed 4 years ago
3
Outputfile(.phy) couldn't be open by Phylip and FastTree

#25 liurongbio closed 4 years ago
3
the result consists of the character of "RY".

#24 U201412486 closed 4 years ago
5
alt allele assignment for heterozygous SNP site instead of IUPAC codes

#23 kumarsaurabh20 closed 4 years ago
4
Add --version flag

#22 tseemann closed 4 years ago
2
Ensure python3 is used

#21 tseemann closed 4 years ago
0
Ensure python3 is used

#20 tseemann closed 4 years ago
1
AttributeError: 'str' object has no attribute 'decode'

#19 joswald closed 4 years ago
6
python3 compat

#18 danielecook closed 4 years ago
0
convert to vcf to interleaved phylip format?

#17 k-sanchez closed 4 years ago
4
Plans to port to python3 ?

#16 tseemann closed 4 years ago
5
Is there a way to get vcf2phylip to output the REF for non-variant positions rather than N?

#15 richarddhaigh closed 5 years ago
6
genotypes excluded even if missing data is less than -m 4

#14 a2g1n closed 4 years ago
9
IndexError: string index out of range

#13 maernster closed 5 years ago
14
printing faulty VCF lines

#12 noahaus closed 5 years ago
1
Key Error '-'

#11 mwpil closed 5 years ago
3
all SNPs were removed when converting my vcf file by using vcf2phylip

#10 yiranzou12138 closed 5 years ago
4
vcf file (monomorphic SNPs discarded) to phylip

#9 Carol-Symbiomics closed 5 years ago
5
error with using python 3

#8 yimingweng closed 5 years ago
1
Getting an error on vcf2phylip

#7 NLRivera1 closed 5 years ago
2
Using with Phylip

#6 mayasheth closed 5 years ago
2
Reduced number of SNPs in the output file

#5 abcosta closed 6 years ago
10
KeyError: '2'

#4 matnguyen closed 6 years ago
6
SyntaxError: invalid syntax

#3 hannahhalp closed 6 years ago
3
Index Error: string out of range

#2 lfall1 closed 6 years ago
2