Example workflow mentions variants.sh, but it could not be found

[toddajohnson]

Is there supposed to be a script variants.sh among the regtools code? It is mentioned in the the example workflow, but I could not find it in the regtools directories or after searching Github.

[kcotto]

Hi @toddajohnson. That was an oversight on our part. I just added it to the scripts directory (https://github.com/griffithlab/regtools/blob/master/scripts/variants.sh). Thanks for reaching out to us about this!

[toddajohnson]

Hi @kcotto , I just ran variants.sh against the tsv files output from cis-splice-effects identify (with -o argument), and the variant_info column is column 18 in the tsv, but the first line of variants.sh extracts the column 17 (transcripts column):
awk 'NR>1 {print $17}' $1 > $2

[kcotto]

Hi @toddajohnson, I just responded to your post #153. But your fix of using the 18th column is correct.