integrative genomics viewer
下载： http://www.broadinstitute.org/igv/download 下载前要注册
导入参考基因组：http://www.broadinstitute.org/software/igv/LoadGenome
Genomes, load a fasta or .genome file
注意fasta文件必须有index
查看vcf文件，直接将vcf文件拖入界面即可
http://www.broadinstitute.org/software/igv/viewing_vcf_files
最上面深蓝和红色的显示的是allele fraction for a single locus
下面描述的是各个样品的snp情况。其中深蓝表示杂合， 蓝绿代表纯合， 灰色代表reference
点击右键会弹出一些选项， 可以根据自己的情况进行选择
vcf文件也需要建立index
查看比对文件，无论是bam还是sam都需要有index， bai or sai, 直接将bam文件拖入查看。
http://www.broadinstitute.org/software/igv/AlignmentData
At higher resolutions read bases that do not match the reference are color coded, and insertions () and deletions relative to the reference become visible. By default, read bases that match are displayed in gray.
Note that alignments that are displayed with light gray borders and white fill, as shown in the following screenshot, have a mapping quality equal to zero. This value (0) means the read could also be mapped to another location.
by freemao
FAFU.