Call SNP用MUMmer

Mummer (NUCmer)通过比较基因组获取突变信息。NUCmer，该方法适合多个近缘物种的基因组比较。

NUCmer is a Perl script pipeline for the alignment of multiple closely related nucleotide sequences.

文献：这是老牌软件

MUMmer 1.0
Alignment of Whole Genomes. Nucleic Acids Research 1999
MUMmer 2.1, NUCmer, and PROmer
Fast Algorithms for Large-scale Genome Alignment and Comparision. Nucleic Acids Research 2002
MUMmer 3.0
Versatile and open software for comparing large genomes. Genome Biology 2004
MUMmer4
A fast and versatile genome alignment system. PLoS Comput Biol. 2018

软件地址

sourceforge: http://mummer.sourceforge.net/
Manual: http://mummer.sourceforge.net/examples/
MUMmer3 manual: http://mummer.sourceforge.net/manual/

Mummer

软件获取

conda create -n mummer
conda activate mummer
conda install -c bioconda mummer
mummer -help
nucmer -help

1 比对:

nucmer -p [out_index] [ref] [query]

nucmer -p align ref.fna input.fna

-p|prefix：Set the prefix of the output files (default "out")
--mum: Use anchor matches that are unique in both the reference and query

2 过滤：

重复序列可能会掩盖可能的SNP，所以使用delta-filter去除一对多、多对多中的冗余匹配

delta-filter -q align.delta > align_q.filter
delta-filter -1 -q -r align.delta > align_qr.filter

-q: 输入序列最佳匹配
Maps each position of each query to its best hit in the reference
-r: 参考序列最佳匹配
Maps each position of each reference to its best hit in the query
-1: intersection of -r and -q alignments 交集
-m: union of -r and -q alignments 并集

3 coord比对/过滤结果：

show-coords -rcl align.delta > align.coords
show-coords -rcl align_q.filter > align_q.coords
show-coords -rcl align_qr.filter > align_qr.coords

-r: 以参考序列排序
Sort output lines by reference IDs and coordinates
-c: 展示覆盖率
Include percent coverage information in the output
-l: 展示序列长度
Include the sequence length information in the output

可见，每次过滤都会减少比对数量

S1 参考匹配序列起点
E1 参考匹配序列终点
S2 输入匹配序列起点
E2 输入匹配序列终点
LEN 1 参考匹配序列长度
LEN 2 输入匹配序列长度
% IDY 匹配序列一致性
LEN R 参考匹配序列所在scaffold/contig长度
LEN Q 输入匹配序列所在scaffold/contig长度
COV R 参考匹配序列长度 vs 所在scaffold/contig长度
COV Q 输入匹配序列长度 vs 所在scaffold/contig长度
TAGS 所在scaffold/contig编号

4 抽查比对结果：

show-aligns [align] [ref seq id] [quary seq id]

show-aligns align.delta NC_009614.1 AF04-12.Scaf1 > check.txt
show-aligns align_q.filter NC_009614.1 AF04-12.Scaf1 > check_q.txt
show-aligns align_qr.filter NC_009614.1 AF04-12.Scaf1 > check_qr.txt

5 query向参考回贴:

show-tiling align.delta > align.tiling
show-tiling align_q.filter > align_q.tiling
show-tiling align_qr.filter > align_qr.tiling

6 call SNPs

show-snps -Clr align.delta > align.snps
show-snps -Clr align_q.filter > align_q.snps
show-snps -Clr align_qr.filter > align_qr.snps

-C: 指输出唯一匹配的snp
Do not report SNPs from alignments with an ambiguous mapping, i.e. only report SNPs where the [R] and [Q] columns equal 0 and do not output these columns
-l: 输出结果中包括序列的长度
Include sequence length information in the output
-r: 按照 ref的ID和snp位置信息进行排序
Sort output lines by reference IDs and SNP positions
-H Do not print the output header
-I Do not report indels
-T Switch to tab-delimited format

质控后SNP数量增加了

P1 参考序列位置
SUB 替换方式
P2 输入序列位置
BUFF
DIST
LEN R 参考序列长度
LEN Q 输入序列长度
FRM forward reverse模式
TAGS 序列编号

插入缺失 indel

参考：
compare two incomplete whole genomes to find the SNP calls?
SNPs detection between two bacterial genomes ?
使用nucmer进行全基因组序列比对
MUMmer共线性分析与SNP检测
MUMMER 两个基因组间比较
SNP，SNV 傻傻分不清楚？
Indel (Insertion and Deletion)分析简介
SNP单核苷酸多态性跟点突变有什么区别？