Update README.md

add usage
treangenlab · May 22, 2023 · 5b8b437 · 5b8b437
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 ## Usage
 ### Example 
-Step 1: Run MethPhaser to get block relationship 
+Step 1: Run MethPhaser to get block relationship. MethPhaser default ignores the largest unphased region (`-ml -1`), if the input data does not contain any large poorly mapped region like centromere, please use `-ml -2` to not ignore any gap. 
 
   ./meth_phaser_parallel -b test_data/HLA.R10.haplotagged.bam -r test_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr6.fna -g test_data/LSK.filtered.gtf -vc test_data/HLA.R10.phased.vcf.gz -o test_data/work