readme

README.md

 > 
 > E-mail：18110700050@fudan.edu.cn
 > 
-> Git: <http://choppy.3steps.cn/renluyao/Quality_control>
+> Git: http://choppy.3steps.cn/renluyao/Quality_control.git
 > 
 > Last Updates: 30/8/2019
 
 ## 流程与参数
 ![](./pictures/workflow.png)
 
+###1. 原始数据质量控制
+
 #### [Fastqc](<https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>)
 
+FastQC是一个常用的测序原始数据的质控软件，主要包括12个模块，具体请参考[Fastqc模块详情](<https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/>)。
+
 ```bash
 fastqc -t <threads> -o <output_directory> <fastq_file>
 ```
 
 #### [Fastq Screen](<https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/>)
 
+Fastq Screen是检测测序原始数据中是否引⼊入其他物种，或是接头引物等污染，⽐比如，如果测序样本
+是⼈人类，我们期望99%以上的reads匹配到⼈人类基因组，10%左右的reads匹配到与⼈人类基因组同源性
+较⾼高的⼩小⿏鼠上。如果有过多的reads匹配到Ecoli或者Yeast，要考虑是否在培养细胞的时候细胞系被污
+染，或者建库时⽂文库被污染。
+
 ````bash
 fastq_screen --aligner <aligner> --conf <config_file> --top <number_of_reads> --threads <threads> <fastq_file>
 ````
 
+`--conf` conifg 文件主要输入了多个物种的fasta文件地址，可根据自己自己的需求下载其他物种的fasta文件加入分析
+
+`--top`一般不需要对整个fastq文件进行检索，取前100000行
+
+``
+
+###2. 比对后数据质量控制
+
 #### [Qualimap](<http://qualimap.bioinfo.cipf.es/>)
 
 ```bash
 qualimap bamqc -bam <bam_file> -outformat PDF:HTML -nt <threads> -outdir <output_directory> --java-mem-size=32G 
 ```
 
+###3. 突变检出数据质量控制
+
 #### [Hap.py](<https://github.com/Illumina/hap.py>)
 
 ```bash

inputSamplesFileExamples.tsv

 oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL5_R1.fastq.gz	oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL5_R2.fastq.gz	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Dedup/Fudan_DNA_LCL5.sorted.deduped.bam	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Dedup/Fudan_DNA_LCL5.sorted.deduped.bam.bai	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Haplotyper/Fudan_DNA_LCL5_hc.vcf	LCL5
-oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R1.fastq.gz	oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R2.fastq.gz	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam.bai	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Haplotyper/Fudan_DNA_LCL6_hc.vcf	LCL6
+oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R1.fastq.gz	oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R2.fastq.gz	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam.bai	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Haplotyper/Fudan_DNA_LCL6_hc.vcf	LCL6