ReadMe_Step1_GenRef.md

Step 1:

Aquila/bin/Aquila_step1_GenRef.py --bam_file possorted_bam.bam --vcf_file ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --chr_start 21 --chr_end 21 --sample_name S12878 --out_dir Assembly_results_S12878 --uniq_map_dir Aquila/Uniqness_map_hg19 

*Required parameters

--bam_file: "possorted_bam.bam" is bam file generated from barcode-awere aligner like "Lonranger align". How to get bam file, you can also check here.

--vcf_file: "ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" is VCF file of chr21 from 1000 Genomes Phase3.

*Optional parameters are the same as "Aquila_step1.py"

Step 2: use "Aquila_step2.py"