IDP-ASE(haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing)VCF File GPD File in Extended Format.

• Prepare necessary input files （http://www.cnblogs.com/renping/p/7488170.html）（http://www.cnblogs.com/renping/p/7391028.html ）

1. VCF File
2. GPD File in Extended Format. You can utilize the accompanying script to convert from regular GPD to extended GPD.

    julia ~/.julia/v0.4/IDPASE/scripts/convert_gpd.jl mygpd.gpd > newgpd.gpd

3. PSL alignment file of your hybrid-Seq data. You can convert from SAM/BAM to psl using libraries such as Au-public utilties in particular the sam_to_psl.py script.
4. FASTQ file of your hybrid-Seq data

      Annotation fileGenepred file in extended format

      VCF fileList of biallelic, exonic SNPs in VCF format -------（#通过ANNOVAR对all_snp.vcf文件进行注释得到）

IDP-ASE(haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing)VCF File GPD File in Extended Format.

原文：http://www.cnblogs.com/linglingtingfei/p/7612791.html