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join snp list

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
rna-seq snp
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updated by Bioaln Bioaln • written by mra8187 • mra8187

Which operating system are you using?

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written by WouterDeCoster 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?

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written by WouterDeCoster WouterDeCoster

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

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written by mra8187 • mra8187

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

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written by WouterDeCoster WouterDeCoster

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

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written by mra8187 • mra8187

1 answer

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.

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written by Bioaln Bioaln

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