A toolkit for tissue specific variant effect prediction
usage: tsva.py [-h] --tissue TISSUE [TISSUE ...] [--verbose] [--list] vep gtex output
positional arguments:
vep VEP result file name (generated by the VEP)
gtex Tissue specific RPKM (based on GTEx)
output output file name
optional arguments:
-h, --help show this help message and exit
--tissue TISSUE [TISSUE ...]
which tissue to use
--verbose use this flag to get more details for variants
--list use this flag to show the full list of tissues supported so far
TSVA can do tissue specific annotation for 30 different tissues and even more sub-tissues! Please see the following list for all supported tissues so far:
Adipose Tissue
Adipose - Subcutaneous
Adipose - Visceral
Adrenal Gland
Adrenal Gland
Bladder
Bladder
Blood
Whole Blood
Cells - EBV-transformed lymphocytes
Blood Vessel
Artery - Tibial
Artery - Aorta
Artery - Coronary
Brain
Brain - Hippocampus
Brain - Hypothalamus
Brain - Cerebellar Hemisphere
Brain - Nucleus accumbens
Brain - Amygdala
Brain - Frontal Cortex
Brain - Substantia nigra
Brain - Anterior cingulate cortex
Brain - Cerebellum
Brain - Caudate
Brain - Spinal cord
Brain - Putamen
Brain - Cortex
Breast
Breast - Mammary Tissue
Cervix Uteri
Cervix - Ectocervix
Cervix - Endocervix
Colon
Colon - Transverse
Colon - Sigmoid
Esophagus
Esophagus - Muscularis
Esophagus - Mucosa
Esophagus - Gastroesophageal Junction
Fallopian Tube
Fallopian Tube
Heart
Heart - Left Ventricle
Heart - Atrial Appendage
Kidney
Kidney - Cortex
Liver
Liver
Lung
Lung
Muscle
Muscle - Skeletal
Nerve
Nerve - Tibial
Ovary
Ovary
Pancreas
Pancreas
Pituitary
Pituitary
Prostate
Prostate
Salivary Gland
Minor Salivary Gland
Skin
Cells - Transformed fibroblasts
Skin - Not Sun Exposed
Skin - Sun Exposed
Small Intestine
Small Intestine - Terminal Ileum
Spleen
Spleen
Stomach
Stomach
Testis
Testis
Thyroid
Thyroid
Uterus
Uterus
Vagina
Vagina