This command-line tool (script) uses phylogenetic information to infer false negative rates in mitochondrial genome data from high-throughput sequencing experiments using estimates of haplogroup assignments using the haplogrep algorithm (doi: 10.1002/humu.21382).
usage: hap_tool.py [-h] [-ana <ana>] [-ft <ft>] -file [<file> [<file> ...]]
This script uses phylotree information to:
- return chrM in FASTA format
- estimate haplogroup
- estimate false negative call rates
- return all loci which should have a SNP
optional arguments:
-h, --help show this help message and exit
-ana <ana> analysis type; fasta, haplogroup, FN_rate, FN_locus
-ft <ft> file type; vcf-hg19, vcf-grch37, var
-file [<file> [<file> ...]]
input file, .vcf or .var
For example, you can use one of the tester files to estimate its haplogroup:
$ python hap_tool.py -ana haplogroup -ft vcf-hg19 -file FreeBayes.vcf
FreeBayes.vcf: K1a4a1a+195; 0.912856941806
The script will return the haplogroup and its score - the higher the better in terms of the quality of the assignment.