I have reference genome and four sample assembly genomes. The sample genomes were mapped to reference genome using BWA and SAMTOOL. Then, I used GATK haplotype caller and got the four SNP VCF files. Because I am interested in one target gene located on chromosome 18. I extracted SNPs around the gene from ch18 and get new four VCF files. Based on the new SNP vcf file, I would like to make a phylogenetic tree using TASSEL(version5). However, I am not sure using TASSEL could generate tree and the manual of TASSEL does not describe how make a tree. Does anyone have that experience? Any suggestion would be very appreciated! Thank you!
Jenny Dong
I don't know about TASSEL. Hope this will help you.
https://vcf-kit.readthedocs.io/en/latest/phylo/
Hi Sureshkumar, thank you for your generous sharing! I will try phyl. It looks very easy to work with! Thanks! I will keep update you once it works! Sureshkumar v.
Hi, Harshit Kumar
. Thank you very much for your suggestion. Tassel accepts VCF file which I have right now. I will download the Tassel on the computer and upload the vcf file into the Tassel and make a tree from there.
Sureshkumar v. Hi. I try to install VCF kit in our lab local server. I installed bwa, samtools, blast, muscle, bcftools, vcf. After that, I run "bcftools filter --set-GTs . --exclude 'FMT/DP < 20' SRX1149858.output-hc.vcf | vk phylo fasta -". The result showed that "bash: vk: command not found". Is there a way to solve the problem? Thank you very much!
Jenny Dong
I think problem in VCF-kit installation.
https://vcf-kit.readthedocs.io/en/latest/
Follow this. After completing the installation, check vk where it was installed.
Again if you facing problem, message me.
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