Hi,
I've got illumina data from a number of human samples that I know are related (hopefully distantly enough to have informative differences) and would like to build a phylogenetic tree using SNP and short INDEL calls etc from GATK, samtools, dindel or similar.
A program that can make use of loads both homozygous and heterozygous variants (and both substitutions and indels) preferably in vcf format would be great!
Ok there might not be such a program though ...
... could anyone point me in the right direction?
I've got illumina data from a number of human samples that I know are related (hopefully distantly enough to have informative differences) and would like to build a phylogenetic tree using SNP and short INDEL calls etc from GATK, samtools, dindel or similar.
A program that can make use of loads both homozygous and heterozygous variants (and both substitutions and indels) preferably in vcf format would be great!
Ok there might not be such a program though ...
... could anyone point me in the right direction?
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