Issue with running muli-plot option

[tania-k]

Hello,
Would you mind clarifying what your list is asking for in your drawing muli-plot option?
When I add a file with one column of just my species ID that is also present in my vcf file I receive this error:

FileList Format wrong, should be (Two columns) :
Stat.FilePath.stat.gz PopulationIDA

What do the "Stat.FilePath.stat.gz" files look like? Are these zipped DNA files of each species and the path they are found in?

Thank you for your time.
Tania

[tania-k]

To those who took some time to find this.
The instructions are buried in the help option.

2). Muti population
This is common situation in the LD decay analysis. For example, if there are 50 samples (wild1, wild2, wild3...wild25, cul1, cul2, cul3...cul25) in the VCF file,
To compare the LD decay of these two groups (wild vs cultivation), first of all, put their sample names into own file list for each group, column or row is ok.

         ./bin/PopLDdecay -InVCF  In.vcf.gz  -OutStat  wild.stat.gz  -SubPop wildName.list
         ./bin/PopLDdecay -InVCF  In.vcf.gz  -OutStat   cul.stat.gz  -SubPop culName.list
         #   created manually  muti.list by yourself
         perl bin/Plot_MutiPop.pl -inList  muti.list  -output  OutputPrefix

Note:
  A. The <wildName.list> can list as follow(column or row is ok):
                  wild1
                  wild2
                  ...
                  wild25
  B. The format of <muti.list> had two columns, the file path of population result and the population flag, such as:
                  /ifshk7/BC_PS/Lddecay/wild.stat.gz   wild
                  /ifshk7/BC_PS/Lddecay/cul.stat.gz    cultivation

3). One population with multi-chr
One population with multiple chromosome VCF files. For example, if there are 3 chromosomes VCF files (Chr1, Chr2 and Chr3) as the input.

        ./bin/PopLDdecay -InVCF  Chr1.vcf.gz  -OutStat  Chr1.stat.gz
        ./bin/PopLDdecay -InVCF  Chr2.vcf.gz  -OutStat  Chr2.stat.gz
        ./bin/PopLDdecay -InVCF  Chr3.vcf.gz  -OutStat  Chr3.stat.gz
        ls  `pwd`/Chr*.stat.gz   > chr.list
        perl bin/Plot_OnePop.pl -inList  chr.list  -output  OutputPrefix

Note:
A. It can run in parallel when calculating the chromosomes' statistics files.
B. The files list only store the file path, which is diff with the multi-population list
C. It will generate the file 'OutputPrefix.bin' is the summary statistics file of all chromosomes, and same format with the chromosomes' statistics files.
D. The <chr.list> format can be generated by as above command 'ls Chr*.stat.gz > chr.list'

4). Muti population with multi-chr
Muti population with multiple chromosome VCF files. For example, if there are 2 chromosomes VCF files (Chr1, Chr2) as the input.

         ./bin/PopLDdecay -InVCF  Chr1.vcf.gz  -OutStat  W.Chr1.stat.gz -SubPop wildName.list
         ./bin/PopLDdecay -InVCF  Chr2.vcf.gz  -OutStat  W.Chr2.stat.gz -SubPop wildName.list
         ./bin/PopLDdecay -InVCF  Chr1.vcf.gz  -OutStat  C.Chr1.stat.gz -SubPop culName.list
         ./bin/PopLDdecay -InVCF  Chr2.vcf.gz  -OutStat  C.Chr2.stat.gz -SubPop culName.list
         ls  `pwd`/W.Chr*.stat.gz   > W.chr.list
         perl bin/Plot_OnePop.pl -inList  W.chr.list  -output  Wild.cat
         ls  `pwd`/C.Chr*.stat.gz   > C.chr.list
         perl bin/Plot_OnePop.pl -inList  C.chr.list  -output  Cul.cat
         perl bin/Plot_MutiPop.pl -inList  muti.list  -output  OutputPrefix

Note:
 A. The format of <muti.list> had two columns , the file path of population result and the population flag, such as:
                  /ifshk7/BC_PS/Lddecay/Wild.cat.bin    wild
                  /ifshk7/BC_PS/Lddecay/Cul.cat.bin     cultivation

[hewm2008]

thanks for using