chr1    249250621

chr2    243199373

chr3    198022430

chr4    191154276

chr5    180915260

chr6    171115067

chr7    159138663

chr8    146364022

chr9    141213431

chr10   135534747

chr11   135006516

chr12   133851895

chr13   115169878

chr14   107349540

chr15   102531392

chr16   90354753

chr17   81195210

chr18   78077248

chr19   59128983

chr20   63025520

chr21   48129895

chr22   51304566

chrX    155270560

chrY    59373566

bedtools nuc -fi genome.fa   -bed hg19_300.bed | cut -f 1-3,5 >  300.gc.bed

7；计算每个bin中比对上的reads counts

bedtools coverage  -abam Sample.bam -b hg19_300.bed > Sample.counts

8:关于的loess回归我只是简单的写了个程序并计算了样本的染色体z_score，小伙伴们要是需要可以跟我索取代码。本来想把代码贴在这里，果断不行，各种符号就没有了。

说明：1:计算z_score的公司来自文献：2011-Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study

2:GC矫正使用的公式来自文献：2013-Non-invasive prenatal diagnostics of aneuploidy using next-generation DNA sequencing technologies, and clinical considerations

3:比对质量 bam文件的质控来自文献：2013- Feasibility Study of Semiconductor Sequencing for Noninvasive Prenatal Detection of Fetal Aneuploidy

4:另外还有一个专门用来分析产前诊断的R软件包,可以参考：2014-RAPIDR an analysis package for non-invasive prenatal testing of aneuploidy

5:关于 loess回归参考一下博文学习就差不多了：http://cos.name/2008/11/lowess-to-explore-bivariate-correlation-by-yihui/#more-57（谢益辉大牛的博客文章拜读）