Updated: May 17, 2021

easy_haplotyper

Usage:

./run.sh

In run.sh, only haplotyper.py is used

• -fs option: target sam file to analyze
• -pos option: target phasing positions, should start with chr_name, follow by positions, separated with colons (e.g. "chr17:51720:53080")
• -fo option: output phasing report

In default, phase_report.tsv will be generated after running run.sh.

haplotyper.py also supports phasing with more than two positions (e.g. "chr17:51720:53080:54007:55368"). Multiple phasing in one run or phasing with pair-end reads are not supported currently.