求助哪位大神知道全外显子测序的流程和原理呀，看了文献中的过程，有部分内容不是特别理解，问题可能比较多，求大神路过指教啊。

Whole exome sequencing on the proband and both her parents was performed by Perkin Elmer using the  llumina Hiseq 2000 machine for 100 bp Paired end sequencing (Instrument control software 1.4.8; RTA  ersion 1.12.4.2). 

1. "100 bp Paired end sequencing"怎么理解呢？

Following targeted enrichment using the SureSelect (Agilent Technologies Canada Inc.) 50Mb v3 Capture kit, we obtained a yield of 20‐22 Gb of sequence data (~84.000.000 reads) per individual. 

2. “Following targeted enrichment” 目标富集是什么意思呢？

The mean exome coverage was 89 fold, with at least 80% of the exome covered more than 30 times. 

3. “fold”是什么意思呢，“at least 80% of the exome covered more than 30 times” 覆盖了至少30倍，这个有什么意义呢？

Mapping to the reference genome sequence (hg19) and alignment was done using both Bowtie and BWA algorithms in order to effectively align reads with substitutions as well as short indels.  The –m 1 option specifies bowtie to discard any reads that can be mapped to more than one location. 

4. “discard any reads that can be mapped to more than one location” 为什么要弃掉map超过一个位点的read呢？不懂原因……

Using samtools, sam.files were then converted to bam.files removing unaligned reads as well as alignments with a quality lower than a Phred quality score at 20 for the entire read.  For local realignment we used the GATK aligner, which searches for missing deletions in Bowtie+BWA  rocedure to reduce false positives. Variant calling was performed by using samtools mpileup.

5.有没有大神大概讲下samtools，GATK aligner给扫下盲？

Single  ucleotide  variants were filtered for minimum mapping quality of a Phred quality score at 30 allowing 99.9% base call accuracy.

6. “a Phred quality score”是什么意思呢？

We deleted non-exonic variants and variants indicated as synonymous to obtain 10.000-15.000 rare (< 0.01 minor allele frequency) or novel variants for each individual. 

7."deleted non-exonic variants"不是全外显子测序吗，为什么还会有非外显子的序列呢？

（Filges I, Manokhina I, Penaherrera M S, et al. Recurrent triploidy due to a failure to complete maternal meiosis II: whole-exome sequencing reveals candidate variants[J]. Mol Hum Reprod,2015,21(4):339-346.）

楼主后面的几个问题都不是简单的文字可以解释给你的，建议楼主和市面上的一些测序公司接触一下，前期可以和销售沟通，等楼主对测序的一些基本知识了解之后，再跟技术支持去沟通一下，当然对于一些生物信息分析方面的内容要和生物信息分析人员沟通才行。所以，你要是想弄明白以上你问的几个问题，单纯的通过发这个帖子肯定是不太现实的，最好的办法就是多跟懂这些知识的人沟通才好。祝好运。