10渐渗片段、INDEL引物、kasp、ssr

Tip

01VCF文件染色体名或样品名替换

渐渗片段

1.查找与参考相同的渐渗片段
# python3 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2/vcf_analyzer_v1.1.py  -i vcf文件 -o 输出目录
# 默认泗棉三号和参考为父母本，策略2
[1]   Running                 python3 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2/vcf_analyzer_v1.1.py   -i all.daerwen.chr-rename.sample-rename.vcf  -o v1.1 &
[2]-  Running                 python3 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2/vcf_analyzer_v1.2.2.py -i all.daerwen.chr-rename.sample-rename.vcf   -o v1.2.2-500k &
[3]+  Running                 python3 /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/method2/vcf_analyzer_v1.2.2.py -i all.daerwen.chr-rename.sample-rename.vcf  -o v1.2.2-5M/ --min-length 5M &

## /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/vcf_reference_identity_analyzer.py 策略1，与参考比较
## /share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/vcf_sample_comparison_analyzer.py 策略1，当前样品与目标样品比较

2.绘制参考来的渐渗片段在染色体上分布
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/fig1_visualize_introgressed_segments.py

3.可不看
1）合并同一样品不同来源渐渗片段
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/merge_genomic_intervals.py
2）绘制同一样品的成分来源
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/fig2_chromosome_region_plotter.py

4.查找不同样品的共有渐渗区段
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/find_common_intervals.py # 首尾一模一样
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/find_overlapping_intervals.py # 允许重叠

kasp标记

0.准备数据
指定样品们
去除非染色体
grep -v  -i "Scaffold"  group2.tm-1.sample-rename.vcf.recode.vcf  > group2.tm-1.onlychr.snp.recode.vcf
去除无差异行
time bcftools view -i 'GT!="0/0" && GT!="0|0"' group2.tm-1.onlychr.snp.recode.vcf > group2.tm-1.onlychr.onlydiff.snp.recode.vcf

接正常kasp流程

5.提取指定区间的基因型数据
## 输入文件是kasp中基因型数据，区间来自于共有渐渗区段
/share/nas1/yuj/script/ddradANDreseqANDgenome/introgressed_fragment/interval_genotype_filter.py

indel标记

路径：
/share/nas2/zhouxy/pipline2/indel-primer-pip/v1.3/indel-primer-pip.pl
/share/nas1/yuj/pipline2/indel-primer-pip/v1.3/ # 更新primer3软件版本

0.准备数据
去除无差异行、去除非染色体的indel vcf文件
grep -v "#" group2.tm-1.onlychr.onlydiff.indel.recode.vcf | cut -f 1,2   > indel.pos.txt
添加#CHR	POS

indel.pos格式如下：
#CHR	POS
A02	39305692
A02	39319333
A02	39319502
A02	39319523
A02	39319664

1.生成命令
perl /share/nas1/yuj/pipline2/indel-primer-pip/v1.3/indel-primer-pip.pl  -i indel.pos.txt    -g  genome.fna  -o  primer_design

2.运行命令
sh primer_design/commands.sh

ssr标记