JBrowser:导入vcf wig和bam数据

samtool view <bam_file>

# tabix: https://github.com/samtools/tabix
# 下载并安装tabix
git clone https://github.com/samtools/tabix.git
cd tabix
make

# 对vcf进行压缩,以s410.vcf为例
$tabix/bgzip s410.vcf

# 建立index
$tabix/tabix -p s410.vcf.gz

# 生成s410.vcf.gz.tbi

[ tracks . s410 ]
storeClass = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate = ../../vcf/s410.vcf.gz
category = VCF
type = JBrowse/View/Track/CanvasVariants
key = s410 VCF1

[ tracks . s410-2 ]
hooks.modify = function( track, feature, div ) { div.style.backgroundColor = track.config.variantIsHeterozygous(feature) ? 'red' : 'blue'; }
key = s410 VCF2
# 区分杂合和纯合位点
variantIsHeterozygous = function( feature ) { var genotypes = feature.get('genotypes');  for( var sampleName in genotypes ) { try { var gtString = genotypes[sampleName].GT.values[0]; if( ! /^1([\|\/]1)*$/.test( gtString) && ! /^0([\|\/]0)*$/.test( gtString ) ) return true; } catch(e) {} } return false; }
storeClass = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate = ../../vcf/s410.vcf.gz
type = JBrowse/View/Track/HTMLVariants
metadata.category = VCF
metadata.Description = Variants called from XX.bam using samtools and bcftools.  Heterozygous variants are shown in red, homozygous variants in blue.

[ tracks . s410_bam ]                     #　以s410.bam为例，要求已经排序并建立index, **.bam.bai文件
style.height = 7
key = BAM - s410 alignment2
storeClass = JBrowse/Store/SeqFeature/BAM
urlTemplate = ../../data/s410.sorted.rmdup.bam
maxFeatureScreenDensity = 4
metadata.category = BAM
metadata.Description = small test pattern of BAM-format paired alignments of simulated resequencing reads on the s410 sample.
type = JBrowse/View/Track/Alignments2
chunkSizeLimit = 50000000                  # 这个是限制在某一个region允许读取的数据量，如果读进的数据量太大会造成浏览器“罢工”。

[ tracks . volvox-sorted_bam_coverage ]
storeClass = JBrowse/Store/SeqFeature/BAM
urlTemplate = ../../data/s410.sorted.rmdup.bam
metadata.category = BAM
metadata.Description = SNP/Coverage view of s410.bam, simulated resequencing alignments.
type = JBrowse/View/Track/SNPCoverage       #注意这个设置的区别
key = BAM - s410 SNPs/Coverage
chunkSizeLimit = 50000000

# 先用samtools把bam转化为sam数据流，再通过管道把数据导入到sam2wig.pl脚本，生成wig文件
samtools view ../data/s410.sorted.rmdup.bam | perl sam2wig.pl --bin 30 --minMQ 30 - > s410.wig

# 下载ucsc tools
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig

# 把wig转化为bigwig格式
./fetchChromSizes hg19 > hg19.chrom.sizes
./wigToBigWig ./s410.wig hg19.chrom.sizes s410.bw

[ tracks . s410_bw_density ]
style.neg_color = function(feature) { return feature.get('score') < 150 ? 'green' : 'red'; } # 如果位点的sequencing depth > 150X显示为红色，否则绿色
bicolor_pivot = mean
key = s410 BigWig Density
storeClass = JBrowse/Store/BigWig
urlTemplate = ../../sam2wig/s410
type = JBrowse/View/Track/Wiggle/Density
metadata.category = Quantitative / Density # 这里是表示两层的分类目录，用/分开。
metadata.Description = Wiggle/Density view of s410.bw.  Also demonstrates use of a user-configurable callback to set the value of neg_color to green when the score is below 150.

[ tracks . s410_bw_xyplot ]
style.pos_color = function(feature) { return feature.get('score') > 30 ? 'red' : 'blue'; }
variance_band = true
key = s410 BigWig XY
storeClass = JBrowse/Store/BigWig
urlTemplate = ../../sam2wig/s410.bw
type = JBrowse/View/Track/Wiggle/XYPlot
metadata.category = Quantitative / XY Plot
metadata.description = Wiggle/XYPlot view of volvox_microarray.bw.  Demonstrates use of a user-configured callback to set the bar color to red when the score is above 30.