从fastq生成vcf文件

流程主要参考 https://github.com/vlkofly/Fastq-to-vcf

1

java -jar $PICARD281 CreateSequenceDictionary R=${ref} O=${ref/fasta/dict}
samtools faidx ${ref}
bwa index ${ref} 

上述三个软件安装很顺利

2

Analyse quality of fastq reads with Fastqc (ver. 0.11.5)
Trim bad quality reads with TRIMMOMATIC (ver. 0.36)
Map reads to the reference with BWA mem (ver. 0.7.15)
Mark duplicates with Picard (ver. 2.8.1)

fastqc安装官网主页已经没有下载链接了，参考https://hpc.ilri.cgiar.org/fastqc-software ，找到下载链接

$ cd /tmp
$ wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip
$ unzip fastqc_v0.11.7.zip
$ sudo cp -r FastQC /export/apps/fastqc/0.11.7
$ sudo chmod +x /export/apps/fastqc/0.11.7/fastqc