I\'m trying to have \" (double quote) inside a pasted command in R
\"
paste(\"perl -ane \'system(\"cat /auto/Sample_output/tmp.$F[0].vcf >> S
Escape " with backslash \. So you will have:
"
\
paste("perl -ane 'system(\"cat /auto/Sample_output/tmp.$F[0].vcf >> Sample_90061.vcf\");'",sep="")