control

对正常人来说，基因组应该是二倍体的，所以凡是测到非2倍体的地方都是CNV。但是CNV本身就是人群遗传物质多样性的体现，所以对癌症样本来说，是需要过滤掉正常人体内的germline的CNV，得到somatic的CNV。

CNV（copy-numbervariant）是指拷贝数目变异，也称拷贝数目多态性（copy-number polymorphism，CNP），是一个大小介于1kb至3MB的DNA片段的变异，在人类及动植物基因组中广泛分布，其覆盖的核苷酸总数大大超过单核苷酸多态性（SNP）的总数，极大地丰富了基因组遗传变异的多样性。按照CNV是否致病可分为致病性CNV、非致病性CNV和不明临床意义CNV。

[general], [sample], [control], [BAF] and [target].

B-Allele Frequency. The B-Allele Frequency is a normalized measure of the allelic intensity ratio of two alleles (A and B), such that a BAF of 1 or 0 indicates the complete absence of one of the two alleles (e.g. AA or BB), and a BAF of 0.5 indicates the equal presence of both alleles (e.g. AB).
if you do not intend to calculate BAF profiles and call genotypes, or if you are not running the program on targeted data,后三个参数可以不设置。
参数列表

somatic-CNV/hg38_genomic/hg38.genomic.fa.fai文件处理，自己创建的和服务器上的每条染色体长度是一致的. chrLenFile:file with chromosome lengths; chromosomes that are not in this list won’t be considered by Control-FREEC!

Error: your BED file with coordinates of targeted regions may contain duplicates
Check chromosome 1
Exit Control-FREEC: before reruning sort the BED file with coordinates of the targeted regions and REMOVE DUPLICATED REGIONS

sort -k1,1V -k2,2n -k3,3n -u target_interval.bed > sort.bed

#内部源码分析报错原因int howMuchToDelete = nextStart - start;if (howMuchToDelete<0) {cerr << "Error: your BED file with coordinates of targeted regions does not seem to be sorted\nCheck chromosome "<<chromosome_&

control

对正常人来说，基因组应该是二倍体的，所以凡是测到非2倍体的地方都是CNV。但是CNV本身就是人群遗传物质多样性的体现，所以对癌症样本来说，是需要过滤掉正常人体内的germline的CNV，得到somatic的CNV。

CNV（copy-numbervariant）是指拷贝数目变异，也称拷贝数目多态性（copy-number polymorphism，CNP），是一个大小介于1kb至3MB的DNA片段的变异，在人类及动植物基因组中广泛分布，其覆盖的核苷酸总数大大超过单核苷酸多态性（SNP）的总数，极大地丰富了基因组遗传变异的多样性。按照CNV是否致病可分为致病性CNV、非致病性CNV和不明临床意义CNV。

[general], [sample], [control], [BAF] and [target].

B-Allele Frequency. The B-Allele Frequency is a normalized measure of the allelic intensity ratio of two alleles (A and B), such that a BAF of 1 or 0 indicates the complete absence of one of the two alleles (e.g. AA or BB), and a BAF of 0.5 indicates the equal presence of both alleles (e.g. AB).
if you do not intend to calculate BAF profiles and call genotypes, or if you are not running the program on targeted data,后三个参数可以不设置。
参数列表

somatic-CNV/hg38_genomic/hg38.genomic.fa.fai文件处理，自己创建的和服务器上的每条染色体长度是一致的. chrLenFile:file with chromosome lengths; chromosomes that are not in this list won’t be considered by Control-FREEC!

Error: your BED file with coordinates of targeted regions may contain duplicates
Check chromosome 1
Exit Control-FREEC: before reruning sort the BED file with coordinates of the targeted regions and REMOVE DUPLICATED REGIONS

sort -k1,1V -k2,2n -k3,3n -u target_interval.bed > sort.bed

#内部源码分析报错原因int howMuchToDelete = nextStart - start;if (howMuchToDelete<0) {cerr << "Error: your BED file with coordinates of targeted regions does not seem to be sorted\nCheck chromosome "<<chromosome_&