xiekunwhy/bsa

Bulked-Segregant Analysis using vcf file with or without parents

bsa's Issues

plotting

你好，最近又遇到一个问题，在画图那一步关于 ‘-cg’ gap between chromosomes [0]这个参数 我设置了几个值发现结果并没有差异，我想让点图染色体之间有一定的间隔，但是通过这个参数好像设置不了，不知道是什么原因，下面是我的代码

# Index 
perl $BSA/point_line_plot.pl -k test.index -f $REF -od ./ -lf snp3.index.mean.xls \ 
       -lp 1,4 -lv 7 -lc "black" \ -pf snp2.index.filter.xls \ 
       -pp 1,2 -pv 5 -cp 0.5 -lwd 2 -pc "#FF8888,#FFA488,#FFBB66,#FFDD55,#FFFF77” \ 
       -hl 0.204 -hc "#424242" -ht 2 -cg 5 -bdc "#FFFFFF" \ 
       -ym 0 -yx 2 -xl "" -yl "expression(Delta(SNPindex))" -las 2 \ 
       -rb /data/Erick_Tong/software/miniconda3/envs/R/bin/Rscript

Use of uninitialized value $cisout[1] in join or string at /opt/bsa/bsaindex.pl line 377, <$fin> line 92.

This is my command line, I don't know what's wrong, I just want to count the values of snpindex greater than 0.8, and I want to graph them.

sbatch -p cpu -n 4 --nodes 1 --job-name cisim -e cisim.err -o cisim.out --wrap "apptainer run /cluster/home/baishenglong/softwares/apptainer_hub/bsa_2023.sif perl /opt/bsa/simulation_v2.pl -k bsa -od result -pt f2 -sd od -s2 21 -md 5 -xd 1000 -mi 0.8 -rb /opt/conda/bin/Rscript"

sbatch -p cpu -n 4 --nodes 1 --job-name mut -e mut.err -o mut.out --wrap "apptainer run /cluster/home/baishenglong/softwares/apptainer_hub/bsa_2023.sif perl /opt/bsa/bsaindex.pl -v /cluster/home/fanrong/work_lei/BSA/02_ZS/03_merge_GVCF/merge.snp_idl.2allele.resume.vcf.gz -k bsa -od result -b2 D_ZS -b1 D_AK58 -p1 D_AK58 -pt f2 -md 5 -xd 1000 -pd 5 -mt all -sf ./result/bsa.cisim.xls -id F -mi 0.8"

bsa-seq

你好，最近利用你写的脚本BSA进行分析，用的果树F1代群体，但是用f1参数过滤后就只有一两个染色体上有数据了，换成其他群体过滤就正常，不知道具体是什么原因，请教一下，如果能给一个联系方式交流就更好了