indraniel

#!/bin/bash

BASE=/gscmnt/gc2802/halllab/idas/laboratory/yaps2-cadd-vep-test

VIRTUALENV=${BASE}/test-venv
source ${VIRTUALENV}/bin/activate

# see confluence
export BMETRICA_DSN="mysql://USER:PASSWORD@hostname:port/database"

indraniel

#!/bin/bash

BASE=/gscmnt/gc2802/halllab/idas/laboratory/yaps2-cadd-vep-test
BCFTOOLS=/gscmnt/gc2719/halllab/bin/bcftools
BGZIP=/gscmnt/gc2802/halllab/idas/software/vep/local/htslib-1.3.2/bin/bgzip
TABIX=/gscmnt/gc2802/halllab/idas/software/vep/local/htslib-1.3.2/bin/tabix

mkdir -p ${BASE}/data/derived/1-create-test-postvqsr-input-data-file/test-vcfs

# cat /gscmnt/gc2802/halllab/idas/jira/BIO-2197/data/derived/7-create-postvqsr-input-data-file/dataset.tsv \

indraniel

#!/usr/bin/env python

# This is a script to merge multiple [GATK][0] Report (or [GATKReport][1])
# files into a single report file.  This is useful when one is running multiple
# GATK commands on a partitioned [VCF][2] data set for performance reasons, and then
# afterwards assembling up the overall output.
#
# Currently this script supports the GATKReports for the following
# [VariantEval][3] Evaluation Module [outputs][4]:
#

slowkow

#!/usr/bin/env python
"""
GTF.py
Kamil Slowikowski
December 24, 2013

Read GFF/GTF files. Works with gzip compressed files and pandas.

    http://useast.ensembl.org/info/website/upload/gff.html