目录

简介

客户需要使用hg38基因组进行融合基因的分析及可视化。

目前国内流程暂无针对于hg38基因组的高级分析。

功能

融合基因及分析及可视化。

数据准备

1. somatic的sv检测结果：

*crest.somatic.sv.predSV.txt/*lumpy.somatic.sv.vcf.gz

数据分析

1. 融合基因检测： 

python /PUBLIC/software/CANCER/Module/CancerGenome/Advance/FusionGene.py -i info.list -o ./FusionGenes -s crest

info.list格式：

#样本名 *somatic.sv.predSV.txt
B4T B4T.somatic.sv.predSV.txt
B9T B9T.somatic.sv.predSV.txt

2. 可视化： 

/PUBLIC/software/public/Graphics/circos-0.64/bin/circos -conf PC9_ER.circos.conf -outputfile sample -outputdir ./

conf格式 ： 

karyotype =/PUBLIC/software/public/Graphics/circos-0.64/data/karyotype/karyotype.human.txt
chromosomes_units = 1000000
<colors>
ctx = chr6
itx = chr14
</colors>
<<include ideogram.conf>>
<<include ticks.conf>>
#The remaining content is standard and required.
<image>
<<include etc/image.conf>>
</image>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
data_out_of_range* = trim
<plots>

</plots>
<links>
z      = 50
radius = 0.97r
crest  = 1
bezier_radius        = 0r
bezier_radius_purity = 0.2
<link>
thickness = 10
file     = ./PC9_ER.circos.input 
</link>
</links>

示例脚本： 

/TJNAS01/AFS_RESEQ/Proj/hongxiang/05.AFS/FusionGenes/FusionGenes_crest/PC9_ER/PC9_ER.crest.annotate.sh