1，将UCSC的refFlat.txt转换成bed文件

基因全长bed

/lustre/rde/user/rde_admin/bin/python2 /opt/anaconda2/bin/refFlat2bed.py /lustre/work/user/zhou.yang/project/5-IVD/1_data/bed/refFlat.txt -f > hg19.genes.bed

refFlat.txt文件示例：

image.png

hg19.genes.bed文件示例：

image.png

注：老版本的cnvkit自带的refFlat2bed.py已被skg_convert.py替换；UCSC的/refFlat.txt文件可通过以下命令下载：

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz ./

exon bed

/lustre/rde/user/rde_admin/bin/python2 /opt/anaconda2/bin/refFlat2bed.py /lustre/work/user/zhou.yang/project/5-IVD/1_data/bed/refFlat.txt -e -m > exons.bed

2，根据bam文件推测捕获区间（bed）

/lustre/rde/user/rde_admin/bin/python2 /opt/anaconda2/bin/guess_baits.py bam1 bam2 ... bamN -o guess-panel_baits.bed -a hg19.genes.bed

guess-panel_baits.bed文件示例：

image.png

注：guess_baits.py也是cnvkit自带的

3，基因名字注释

/lustre/rde/user/rde_admin/bin/python2 /lustre/rde/user/rde_admin/bin/cnvkit.py target  guess-panel_baits.100.sample.bed --annotate /lustre/rde/user/rde_admin/database/refFlat/refFlat.txt -o SHR.bed

SHR.bed文件示例：

image.png