join snp list

Question

[mra8187]

Dear all

i am trying to join 2 list of SNPs to find out common SNP's ... whats wrong with my script ?

join‬‬ ‫‪-1‬‬ ‫‪1‬‬ ‫‪-2‬‬ ‫‪1‬‬ ‫‪<( sort‬‬ ‫‪-k1,1‬‬ SNPList1.filtered-D-1.txt) ‫‪<( sort‬‬ ‫‪-k1,1‬‬ SNPList1.filtered-D-2.txt) | sort -V > '/home/mra/Desktop/snps/D/ ‫‪CommonSNPlistD1-2.txt‬‬'

error :

sort‬‬: command not found
join‬‬: command not found
sort‬‬: command not found

[WouterDeCoster]

Which operating system are you using?

[mra8187]

linux mint cinnamon 17

[WouterDeCoster]

It's rather odd that even sort and join are not found on your system. There is nothing wrong with your command, but your operating system can't find the tools it needs. Which should be installed by default if I'm not mistaken.

Can you check your path using echo $PATH?

[mra8187]

thank you for help

echo $PATH /home/mra/miniconda3/bin:/home/mra/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

[WouterDeCoster]

Does it work if you do separately sort‬‬ ‫‪-k1,1‬‬ SNPList1.filtered-D-2.txt without the remaining pipes and parts?

[mra8187]

no didnt work sort‬‬ ‫‪-k1,1‬‬ SNPList1.filtered-D-2.txt sort‬‬: command not found

Answer 1

[Bioaln]

Have you tried the comm command?

It is trivial with that:

comm -12 snplist1.txt snplist2.txt

input files must be sorted, nothing a e.g. <(sort snplist1.txt) couldn't handle.