Hi! I have tried making a dendrogram from a VCF file that contains SNP data for 20 samples. First, I tried the SNP relate software, but it was excluding all the SNPs
SNP pruning based on LD: Excluding 0 SNP on non-autosomes Excluding 78,187 SNPs (monomorphic: TRUE, MAF: 0.1, missing rate: 0.1) Working space: 20 samples, 0 SNP using 1 (CPU) core sliding window: 500,000 basepairs, Inf SNPs |LD| threshold: 1 method: composite 0 markers are selected in total.
Then I have tried the SNPphylo package but it is also based on SNPrelate and I get the same results. Does anyone know a quick solution to getting a dendrogram from a vcf file?
I have also tried making it a fasta file with gatk and tried FastTree but I get this error:
FastTree Version 2.1.10 Double precision (No SSE3) Alignment: trial.fasta Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.80 ML Model: Jukes-Cantor, CAT approximation with 20 rate categories Wrong number of characters for 1: expected 8477918 but have 55489 instead. This sequence may be truncated, or another sequence may be too long.
Also, I don't mind using fasta aglinment files but can anyone explain me how I can get a tree from whole genome sequence files (I have bam files)?