How to convert the bam file to the aligned fasta file and perform the phylogenetic analysis?

Question

[lhaiyan3]

Dear all,

We have a bunch of bam file for the targeted tumor genes sequencing. We want to perform the phylogenetic analysis for these data. Most phylogenetic tools needs the aligned fasta files. Can anyone please give me the suggestions how i can get the aligned fasta files from bam files or other good ways to do the phylogenetic analysis directly using the bam files? Thanks very much for your suggestion.

best

HY

[Michael]

Please explain why you want to do a phylogenetic analysis of tumor sequences. I am not sure this is a good idea in general. Please explain your experimental setup.

[lhaiyan3]

Hi, Michael:

My colleague has the DNA sequencing on a panel of approximately 500 commonly mutated oncogenes.He has two purpose for his experiments:

1. To deduce whether each tumor is genetically a metastatic lesion or if it is an individual tumor
2. To determine genetic and transcriptomic mechanisms of resistance to therapy (some samples are from before therapy and some are from after)

The idea about performing phylogenetic analysis was to show how related different tumors are within one person. He currently has the bam files available. Can anyone give me the suggestions whether it is a good idea to perform this kind of analysis? He finds the Metapiga tools to do this kind of analysis. Thanks.

HY

[Michael]

I think you should base this analysis on genotypes from variant calling only. A conventional multiple alignment based phylogeny would suffer from too many invariant sites. A related question seems to be Tumor evolution tool for reconstructing a phylogenetic tree and Tumor phylogenetic tree software