bin是指分离群体中,没有发生重组的染色体区块
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一般是在群体里采用binmap,单样本snp的012分型只有1(杂合),2(表示另一种等位基因)
###vcf文件过滤
vcftools \
--minDP 4 \
--maxDP 100 \
--minGQ 10 \
--minQ 30 \
--min-meanDP 3 \
--out meanDP3.miss0.5.maf0.01.vcf \
--gzvcf Pop.vcf.gz \
--recode --recode-INFO-all \
--max-missing 0.5 \
--maf 0.01
###vcf转012矩阵
vcftools --gzvcf Pop.vcf.gz --012 --out Pop.012
###矩阵转置
awk '{i=1;while(i <= NF){col[i]=col[i] $i " ";i=i+1}} END {i=1;while(i<=NF){print col[i];i=i+1}}' Pop.012 | sed 's/[ \t]*$//g' > genotype_transpose.txt
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下面是构建binmap部分:
----实际操作就是通过滑窗统计和,比如20个snp一个滑窗,
等于0,即P1的基因型
,
等于20,即P2的基因型
;
杂合一般和在10左右
未完待续
参考:
Meng-Fan Qin, Lei-Ting Li, Jugpreet Singh, Man-Yi Sun, Bing Bai, Si-Wei Li, Jiang-Ping Ni, Jia-Ying Zhang, Xun Zhang, Wei-Lin Wei, Ming-Yue Zhang, Jia-Ming Li, Kai-Jie Qi, Shao-Ling Zhang, Awais Khan, Jun Wu, Construction of a high-density bin-map and identification of fruit quality-related quantitative trait loci and functional genes in pear, Horticulture Research, Volume 9, 2022, uhac141, https://doi.org/10.1093/hr/uhac141
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