ASM

ASM（allele-specific methylation analysis）

Title: ASM Date: 2019-02-18 Category: methyl Tags: methyl, ASM Author: shaohuaihan Summary: for allele-specific methylation analysis

程序功能及原理说明

ASM (allele-specific methylation analysis) is an allele specific methylation analysis is primarily to compare the DNA methylation linked by two different alleles (heterozygous genotype).

ASM works for SNP files in standard VCF format, however, may be ok for Bis-SNP output. If it does not work, you’d better reformat the Bis-SNP results.

examples allele-specific methylated region shown in Weilong Guo, et al., Scientifc Report, 2016

程序使用说明

$bash run_ASM.sh 

ASM: Allele specific methylated region/site calling
    Fisher exact test for site calling
    Students' t-test for region calling


USAGE: run_ASM.sh <ref_FA>  <align_BAM>  <snp_VCF>  <out_Folder>
need SAMtools and perl

参数说明

ref_FA: 参考基因组FA文件，需要有fai的索引，samtools完成
align_BAM： 比对文件，需要有bai索引，samtools完成
snp_VCF： 标准的VCF文件，若是bisSNP检测，可能需要简单处理一下
其他参数内部默认

使用示例

bash bash run_ASM.sh test.fa test.bam test.vcf ./

shell中将所输入的文件如基因组fa、比对后BAM均连接到输出路径，重新进行索引和后续分析


### ASS（allele specific methylated site）输出示例：
Chr SNP_Pos  Ref    Allele1 Allele2 C_Pos   Allele1_linked_C    Allele2_linked_C    Allele1_linked_C_met    Allele2_linked_C_met    pvalue  fdr ASM
Chr1    8949221 T   T   A   8949252 30,2    6,0 0.94    1.00    1.00e+00    1.00e+00    FALSE
各列信息如下：
Chr: 染色体编号
SNP_Pos: SNP的1-based比对位置
Ref: 参考基因组碱基
Allele1: 等位核苷酸1 [ATCG]
Allele2: 等位核苷酸2 [ATCG]
C_Pos: C的1-based位置
Allele1_linked_C: 与allele1相关联的胞嘧啶的reads深度，逗号分隔，即支持甲基化和非甲基化reads数目
Allele2_linked_C: 与allele2相关联的胞嘧啶的reads深度，逗号分隔，即支持甲基化和非甲基化reads数目
Allele1_linked_C_met: 与allele1关联的C的甲基化水平
Allele2_linked_C_met: 与allele2关联的C的甲基化水平
pvalue: t test得到的p-value
fdr: BH校正后的p-value
ASM: TRUE表示该C是allele特异甲基化的

### ASR（allele specific methylated region）输出示例
Chr Pos Ref Allele1 Allele2 Allele1_linked_C    Allele2_linked_C    Allele1_linked_C_met    Allele2_linked_C_met    pvalue  fdr ASM
chr1    8943402 A   A   T   1-1 0.8-1   1   0.9 5.01e-01    7.52e-01    FALSE
各列信息如下：
Chr: 染色体编号
Pos: SNP的1-based比对位置
Ref: 参考基因组碱基
Allele1: 等位核苷酸1 [ATCG]
Allele2: 等位核苷酸2 [ATCG]
Allele1_linked_C: 与allele1关联的Cs的甲基化水平，"-"分隔
Allele2_linked_C: 与allele2关联的Cs的甲基化水平，"-"分隔
Allele1_linked_C_met: 与allele1关联的Cs的平均甲基化水平
Allele2_linked_C_met: 与allele2关联的Cs的平均甲基化水平
pvalue: t test得到的p-value
fdr: BH校正后的p-value
ASM: TRUE表示该region是allele特异甲基化的

Resource

Weilong Guo, et al. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. 2017, Bioinformatics.