Script used for the haplogroup estimation across smaller variant windows.
Usage: HaplogroupEstimation.py [-h] --sam [SAM file] --vcf [vcf file] --window [window size]
The SAM file can be read from the stdin by using --sam -. The default window size is 35.
The output format is tab seperated and contains the following:
- reference or contig
- Positions in the SNP window (dash seperated)
- haplotype 1
- count of haplotype 1
- haplotype 2
- count of haplotype 2
- etc.
For example:
CP 10571-10577 AT 11 TA 32
CP 10719-10725 TT 14 AG 16