Mercurial > repos > thondeboer > neat_genreads

annotate utilities/deprecated/README.md @ 7:fc1c7b6fb7b6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Tue, 15 May 2018 18:12:29 -0400
parents 6e75a84e9338
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
1 #Deprecated Perl Scripts
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
2 These scripts were updated and rewritten in python to improve ease of use and speed. Usage and a quick description of the deprecated scripts can be found below. Please use genMutModel.py to generate mutation models.
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
3
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
4 ##FindNucleotideContextOnReference.pl
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
5 This script takes in VCF files and generates variant frequency models for NEAT. Coordinates for each variant are located within the HG19 human reference. The corresponding trinucleotide context around that location on the reference is returned into a new column.
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
6
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
7 ## Running the Script
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
8 The script requires 5 arguments to be entered after the full path to FindNucleotideContextOnReference.healthy.pl
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
9
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
10 ```
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
11 1. Full path to Fastahack
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
12 2. Full path to Reference Genome
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
13 3. Full path to input VCF
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
14 4. Full path to output file
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
15 5. Full path to human GFF
6e75a84e9338 planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
thondeboer
parents:
diff changeset
16 ```