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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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SNPs that passed the filters: 0 #45

Closed Peijiawei2022 closed 1 month ago

Peijiawei2022 commented 11 months ago

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 complete VCF file, and the complete VCF file can be converted normally.

edgardomortiz commented 11 months ago

I'm afraid I need more info, how did you extract the 9 samples? can you share a few thousand lines of your9-sample VCF?

Edgardo

Peijiawei2022 commented 11 months ago

vcftools --gzvcf barly_panseq_130_all.cds.maff.rename.snp.vcf.gz --keep simple.txt --recode --stdout | gzip -c > timetree_1.vcf.gz 图片

edgardomortiz commented 11 months ago

The 9 SNPs you shared looked OK, perhaps the problem (if there is one) is further ahead in the file. Unfortunately I can't fix the problem if I don't have a piece of your VCF file (a few thousand lines are OK)

Peijiawei2022 commented 11 months ago

will, just moment I use the latest v2.8, everything is OK. the problem occurs when i use the v2.0,thanks!

edgardomortiz commented 11 months ago

cool