Skip to content

Commit

Permalink
gnomAD_genome_ALL
Browse files Browse the repository at this point in the history
  • Loading branch information
@quanliustc
quanliustc committed Sep 4, 2018
1 parent dfab667 commit a846dea
Show file tree
Hide file tree
Showing 2 changed files with 20 additions and 20 deletions.
34 changes: 17 additions & 17 deletions Intervar.py
View file
Expand Up @@ -11,7 +11,7 @@

prog="InterVar"

version = """%prog 2.0.2 20180118
version = """%prog 2.0.2 20180827
Written by Quan LI,leequan@gmail.com.
InterVar is free for non-commercial use without warranty.
Please contact the authors for commercial use.
Expand Down Expand Up @@ -450,7 +450,7 @@ def check_downdb():
print("Warning: the folder of %s is already created!" % path)
ds=paras['database_names']
ds.expandtabs(1);
# database_names = refGene 1000g2014oct esp6500siv2_all avsnp147 ljb26_all clinvar_20150629 exac03 hg19_dbscsnv11 dbnsfp31a_interpro rmsk ensGene
# database_names = refGene 1000g2014oct esp6500siv2_all avsnp147 ljb26_all clinvar_20150629 gnomad_genome hg19_dbscsnv11 dbnsfp31a_interpro rmsk ensGene
if not os.path.isfile(paras['annotate_variation']):
print("Warning: The Annovar file [ %s ] is not here,please download ANNOVAR firstly: http://www.openbioinformatics.org/annovar"
% paras['annotate_variation'])
Expand Down Expand Up @@ -514,7 +514,7 @@ def check_input():
return

def check_annovar_result():
# table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,ljb26_all,CLINSIG,exac03 -operation g,f,f,f,f,f,f -nastring . -csvout
# table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,ljb26_all,CLINSIG,gnomad_genome -operation g,f,f,f,f,f,f -nastring . -csvout
inputft= paras['inputfile_type']
annovar_options=" "
if re.findall('true',paras['otherinfo'], flags=re.IGNORECASE) :
Expand All @@ -528,18 +528,18 @@ def check_annovar_result():
if paras['skip_annovar'] != True:
sys.exit()
if inputft.lower() == 'avinput' :
cmd="perl "+paras['table_annovar']+" "+paras['inputfile']+" "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ paras['outfile']+" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
cmd="perl "+paras['table_annovar']+" "+paras['inputfile']+" "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ paras['outfile']+" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,gnomad_genome,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
print("%s" %cmd)
os.system(cmd)
if inputft.lower() == 'vcf' :
cmd="perl "+paras['table_annovar']+" "+paras['inputfile']+".avinput "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ paras['outfile']+" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
cmd="perl "+paras['table_annovar']+" "+paras['inputfile']+".avinput "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ paras['outfile']+" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,gnomad_genome,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
print("%s" %cmd)
os.system(cmd)
if inputft.lower() == 'vcf_m' :
for f in glob.iglob(paras['outfile']+"*.avinput"):
print("INFO: Begin to annotate sample file of %s ...." %(f))
new_outfile=re.sub(".avinput","",f)
cmd="perl "+paras['table_annovar']+" "+f+" "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ new_outfile +" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,exac03,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
cmd="perl "+paras['table_annovar']+" "+f+" "+paras['database_locat']+" -buildver "+paras['buildver']+" -remove -out "+ new_outfile +" -protocol refGene,esp6500siv2_all,1000g2015aug_all,avsnp147,dbnsfp33a,clinvar_20170905,gnomad_genome,dbscsnv11,dbnsfp31a_interpro,rmsk,ensGene,knownGene -operation g,f,f,f,f,f,f,f,f,r,g,g -nastring ."+annovar_options
print("%s" %cmd)
os.system(cmd)

Expand Down Expand Up @@ -582,7 +582,7 @@ def check_gdi_rvis_LOF(anvfile):
str = fh.read()
for line in str.split('\n'):
cls=line.split('\t')
rvis['Gene']=['RVIS_ExAC_0.05%(AnyPopn)','%RVIS_ExAC_0.05%(AnyPopn)']
rvis['Gene']=['RVIS_gnomAD_genome_0.05%(AnyPopn)','%RVIS_gnomAD_genome_0.05%(AnyPopn)']
if len(cls)>1:
rvis[cls[4]]=cls[5:]
except IOError:
Expand Down Expand Up @@ -1310,7 +1310,7 @@ def check_BA1(line,Freqs_flgs,Allels_flgs):
'''
BA1=0
cls=line.split('\t')
Freqs_3pops={'1000g2015aug_all':0,'esp6500siv2_all':0,'ExAC_ALL':0}
Freqs_3pops={'1000g2015aug_all':0,'esp6500siv2_all':0,'gnomAD_genome_ALL':0}
for key in Freqs_3pops.keys():
try:
if float(cls[Freqs_flgs[key]])>0.05: BA1=1
Expand Down Expand Up @@ -1351,7 +1351,7 @@ def check_BS2(line,Freqs_flgs,Allels_flgs,Funcanno_flgs):
'''
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked
(hemizygous) disorder, with full penetrance expected at an early age
check ExAC_ALL
check gnomAD_genome_ALL
'''
BS2=0
cls=line.split('\t')
Expand Down Expand Up @@ -1750,7 +1750,7 @@ def assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs):
# end process the user's evidence file

cls=line.split('\t')
if len(cls)>1:#esp6500siv2_all 1000g2015aug_all ExAC_ALL
if len(cls)>1:#esp6500siv2_all 1000g2015aug_all gnomAD_genome_ALL
BP_out=classfy(PVS1,PS,PM,PP,BA1,BS,BP,Allels_flgs,cls)
line_t="%s PVS1=%s PS=%s PM=%s PP=%s BA1=%s BS=%s BP=%s" %(BP_out,PVS1,PS,PM,PP,BA1,BS,BP)

Expand All @@ -1775,10 +1775,10 @@ def my_inter_var(annovar_outfile):
newoutfile=annovar_outfile+".grl_p"
newoutfile2=annovar_outfile+".intervar"

Freqs_flgs={'1000g2015aug_all':0,'esp6500siv2_all':0,'ExAC_ALL':0,'ExAC_AFR':0,'ExAC_AMR':0,'ExAC_EAS':0,'ExAC_FIN':0,'ExAC_NFE':0,'ExAC_OTH':0,'ExAC_SAS':0}
Freqs_flgs={'1000g2015aug_all':0,'esp6500siv2_all':0,'gnomAD_genome_ALL':0,'gnomAD_genome_AFR':0,'gnomAD_genome_AMR':0,'gnomAD_genome_EAS':0,'gnomAD_genome_FIN':0,'gnomAD_genome_NFE':0,'gnomAD_genome_OTH':0,'gnomAD_genome_ASJ':0}
Funcanno_flgs={'Func.refGene':0,'ExonicFunc.refGene':0,'AAChange.refGene':0,'Gene':0,'Gene damage prediction (all disease-causing genes)':0,'CLNDBN':0,'CLNACC':0,'CLNDSDB':0,'dbscSNV_ADA_SCORE':0,'dbscSNV_RF_SCORE':0,'GERP++_RS':0,'LoFtool_percentile':0,'Interpro_domain':0,'rmsk':0,'SIFT_score':0,'phyloP46way_placental':0,'Gene.ensGene':0,'CLINSIG':0,'CADD_raw':0,'CADD_phred':0,'avsnp147':0,'AAChange.ensGene':0,'AAChange.knownGene':0,'MetaSVM_score':0,'Otherinfo':0}
Allels_flgs={'Chr':0,'Start':0,'End':0,'Ref':0,'Alt':0}
# ExAC_ALL esp6500siv2_all 1000g2015aug_all SIFT_score CADD_raw CADD_phred GERP++_RS phyloP46way_placental dbscSNV_ADA_SCORE dbscSNV_RF_SCORE Interpro_domain
# gnomAD_genome_ALL esp6500siv2_all 1000g2015aug_all SIFT_score CADD_raw CADD_phred GERP++_RS phyloP46way_placental dbscSNV_ADA_SCORE dbscSNV_RF_SCORE Interpro_domain

try:
fh=open(newoutfile, "r")
Expand All @@ -1787,9 +1787,9 @@ def my_inter_var(annovar_outfile):
line_sum=0;
print("Notice: Begin the variants interpretation by InterVar ")
if re.findall('true',paras['otherinfo'], flags=re.IGNORECASE) :
fw.write("#%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("Chr","Start","End","Ref","Alt","Ref.Gene","Func.refGene","ExonicFunc.refGene", "Gene.ensGene","avsnp147","AAChange.ensGene","AAChange.refGene","Clinvar","InterVar and Evidence","Freq_ExAC_ALL", "Freq_esp6500siv2_all","Freq_1000g2015aug_all", "CADD_raw","CADD_phred","SIFT_score","GERP++_RS","phyloP46way_placental","dbscSNV_ADA_SCORE", "dbscSNV_RF_SCORE", "Interpro_domain","AAChange.knownGene","rmsk","MetaSVM_score","Freq_ExAC_POPs","OMIM","Phenotype_MIM","OrphaNumber","Orpha","Otherinfo" ))
fw.write("#%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("Chr","Start","End","Ref","Alt","Ref.Gene","Func.refGene","ExonicFunc.refGene", "Gene.ensGene","avsnp147","AAChange.ensGene","AAChange.refGene","Clinvar","InterVar and Evidence","Freq_gnomAD_genome_ALL", "Freq_esp6500siv2_all","Freq_1000g2015aug_all", "CADD_raw","CADD_phred","SIFT_score","GERP++_RS","phyloP46way_placental","dbscSNV_ADA_SCORE", "dbscSNV_RF_SCORE", "Interpro_domain","AAChange.knownGene","rmsk","MetaSVM_score","Freq_gnomAD_genome_POPs","OMIM","Phenotype_MIM","OrphaNumber","Orpha","Otherinfo" ))
else:
fw.write("#%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("Chr","Start","End","Ref","Alt","Ref.Gene","Func.refGene","ExonicFunc.refGene", "Gene.ensGene","avsnp147","AAChange.ensGene","AAChange.refGene","Clinvar","InterVar and Evidence","Freq_ExAC_ALL", "Freq_esp6500siv2_all","Freq_1000g2015aug_all", "CADD_raw","CADD_phred","SIFT_score","GERP++_RS","phyloP46way_placental","dbscSNV_ADA_SCORE", "dbscSNV_RF_SCORE", "Interpro_domain","AAChange.knownGene","rmsk","MetaSVM_score","Freq_ExAC_POPs","OMIM","Phenotype_MIM","OrphaNumber","Orpha" ))
fw.write("#%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("Chr","Start","End","Ref","Alt","Ref.Gene","Func.refGene","ExonicFunc.refGene", "Gene.ensGene","avsnp147","AAChange.ensGene","AAChange.refGene","Clinvar","InterVar and Evidence","Freq_gnomAD_genome_ALL", "Freq_esp6500siv2_all","Freq_1000g2015aug_all", "CADD_raw","CADD_phred","SIFT_score","GERP++_RS","phyloP46way_placental","dbscSNV_ADA_SCORE", "dbscSNV_RF_SCORE", "Interpro_domain","AAChange.knownGene","rmsk","MetaSVM_score","Freq_gnomAD_genome_POPs","OMIM","Phenotype_MIM","OrphaNumber","Orpha" ))

for line in strs.split('\n'):
BP="UNK" # the inter of pathogenetic/benign
Expand All @@ -1809,7 +1809,7 @@ def my_inter_var(annovar_outfile):
clinvar_bp=cls3[0]

intervar_bp=assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs)
Freq_ExAC_POPs="AFR:"+cls[Freqs_flgs['ExAC_AFR']]+",AMR:"+cls[Freqs_flgs['ExAC_AMR']]+",EAS:"+cls[Freqs_flgs['ExAC_EAS']]+",FIN:"+cls[Freqs_flgs['ExAC_FIN']]+",NFE:"+cls[Freqs_flgs['ExAC_NFE']]+",OTH:"+cls[Freqs_flgs['ExAC_OTH']]+",SAS:"+cls[Freqs_flgs['ExAC_SAS']]
Freq_gnomAD_genome_POPs="AFR:"+cls[Freqs_flgs['gnomAD_genome_AFR']]+",AMR:"+cls[Freqs_flgs['gnomAD_genome_AMR']]+",EAS:"+cls[Freqs_flgs['gnomAD_genome_EAS']]+",FIN:"+cls[Freqs_flgs['gnomAD_genome_FIN']]+",NFE:"+cls[Freqs_flgs['gnomAD_genome_NFE']]+",OTH:"+cls[Freqs_flgs['gnomAD_genome_OTH']]+",ASJ:"+cls[Freqs_flgs['gnomAD_genome_ASJ']]
OMIM="."
mim2=mim2gene_dict2.get(cls[Funcanno_flgs['Gene']],".")
mim1=mim2gene_dict.get(cls[Funcanno_flgs['Gene.ensGene']],".")
Expand All @@ -1832,9 +1832,9 @@ def my_inter_var(annovar_outfile):

if re.findall('true',paras['otherinfo'], flags=re.IGNORECASE) :
cls[Funcanno_flgs['Otherinfo']]=cls[Funcanno_flgs['Otherinfo']].replace('\t', ';')
fw.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (cls[Allels_flgs['Chr']],cls[Allels_flgs['Start']],cls[Allels_flgs['End']],cls[Allels_flgs['Ref']],cls[Allels_flgs['Alt']],cls[Funcanno_flgs['Gene']],cls[Funcanno_flgs['Func.refGene']],cls[Funcanno_flgs['ExonicFunc.refGene']], cls[Funcanno_flgs['Gene.ensGene']],cls[Funcanno_flgs['avsnp147']],cls[Funcanno_flgs['AAChange.ensGene']],cls[Funcanno_flgs['AAChange.refGene']],clinvar_bp,intervar_bp,cls[Freqs_flgs['ExAC_ALL']], cls[Freqs_flgs['esp6500siv2_all']], cls[Freqs_flgs['1000g2015aug_all']], cls[Funcanno_flgs['CADD_raw']],cls[Funcanno_flgs['CADD_phred']],cls[Funcanno_flgs['SIFT_score']], cls[Funcanno_flgs['GERP++_RS']],".", cls[Funcanno_flgs['dbscSNV_ADA_SCORE']], cls[Funcanno_flgs['dbscSNV_RF_SCORE']], cls[Funcanno_flgs['Interpro_domain']],cls[Funcanno_flgs['AAChange.knownGene']],cls[Funcanno_flgs['rmsk']],cls[Funcanno_flgs['MetaSVM_score']],Freq_ExAC_POPs,OMIM,Pheno_MIM,orpha,orpha_details,cls[Funcanno_flgs['Otherinfo']] ))
fw.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (cls[Allels_flgs['Chr']],cls[Allels_flgs['Start']],cls[Allels_flgs['End']],cls[Allels_flgs['Ref']],cls[Allels_flgs['Alt']],cls[Funcanno_flgs['Gene']],cls[Funcanno_flgs['Func.refGene']],cls[Funcanno_flgs['ExonicFunc.refGene']], cls[Funcanno_flgs['Gene.ensGene']],cls[Funcanno_flgs['avsnp147']],cls[Funcanno_flgs['AAChange.ensGene']],cls[Funcanno_flgs['AAChange.refGene']],clinvar_bp,intervar_bp,cls[Freqs_flgs['gnomAD_genome_ALL']], cls[Freqs_flgs['esp6500siv2_all']], cls[Freqs_flgs['1000g2015aug_all']], cls[Funcanno_flgs['CADD_raw']],cls[Funcanno_flgs['CADD_phred']],cls[Funcanno_flgs['SIFT_score']], cls[Funcanno_flgs['GERP++_RS']],".", cls[Funcanno_flgs['dbscSNV_ADA_SCORE']], cls[Funcanno_flgs['dbscSNV_RF_SCORE']], cls[Funcanno_flgs['Interpro_domain']],cls[Funcanno_flgs['AAChange.knownGene']],cls[Funcanno_flgs['rmsk']],cls[Funcanno_flgs['MetaSVM_score']],Freq_gnomAD_genome_POPs,OMIM,Pheno_MIM,orpha,orpha_details,cls[Funcanno_flgs['Otherinfo']] ))
else:
fw.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (cls[Allels_flgs['Chr']],cls[Allels_flgs['Start']],cls[Allels_flgs['End']],cls[Allels_flgs['Ref']],cls[Allels_flgs['Alt']],cls[Funcanno_flgs['Gene']],cls[Funcanno_flgs['Func.refGene']],cls[Funcanno_flgs['ExonicFunc.refGene']], cls[Funcanno_flgs['Gene.ensGene']],cls[Funcanno_flgs['avsnp147']],cls[Funcanno_flgs['AAChange.ensGene']],cls[Funcanno_flgs['AAChange.refGene']],clinvar_bp,intervar_bp,cls[Freqs_flgs['ExAC_ALL']], cls[Freqs_flgs['esp6500siv2_all']], cls[Freqs_flgs['1000g2015aug_all']], cls[Funcanno_flgs['CADD_raw']],cls[Funcanno_flgs['CADD_phred']],cls[Funcanno_flgs['SIFT_score']], cls[Funcanno_flgs['GERP++_RS']],".", cls[Funcanno_flgs['dbscSNV_ADA_SCORE']], cls[Funcanno_flgs['dbscSNV_RF_SCORE']], cls[Funcanno_flgs['Interpro_domain']],cls[Funcanno_flgs['AAChange.knownGene']],cls[Funcanno_flgs['rmsk']],cls[Funcanno_flgs['MetaSVM_score']],Freq_ExAC_POPs,OMIM,Pheno_MIM,orpha,orpha_details ))
fw.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tclinvar: %s \t InterVar: %s \t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (cls[Allels_flgs['Chr']],cls[Allels_flgs['Start']],cls[Allels_flgs['End']],cls[Allels_flgs['Ref']],cls[Allels_flgs['Alt']],cls[Funcanno_flgs['Gene']],cls[Funcanno_flgs['Func.refGene']],cls[Funcanno_flgs['ExonicFunc.refGene']], cls[Funcanno_flgs['Gene.ensGene']],cls[Funcanno_flgs['avsnp147']],cls[Funcanno_flgs['AAChange.ensGene']],cls[Funcanno_flgs['AAChange.refGene']],clinvar_bp,intervar_bp,cls[Freqs_flgs['gnomAD_genome_ALL']], cls[Freqs_flgs['esp6500siv2_all']], cls[Freqs_flgs['1000g2015aug_all']], cls[Funcanno_flgs['CADD_raw']],cls[Funcanno_flgs['CADD_phred']],cls[Funcanno_flgs['SIFT_score']], cls[Funcanno_flgs['GERP++_RS']],".", cls[Funcanno_flgs['dbscSNV_ADA_SCORE']], cls[Funcanno_flgs['dbscSNV_RF_SCORE']], cls[Funcanno_flgs['Interpro_domain']],cls[Funcanno_flgs['AAChange.knownGene']],cls[Funcanno_flgs['rmsk']],cls[Funcanno_flgs['MetaSVM_score']],Freq_gnomAD_genome_POPs,OMIM,Pheno_MIM,orpha,orpha_details ))

#print("%s\t%s %s" % (line,clinvar_bp,intervar_bp))

Expand Down
6 changes: 3 additions & 3 deletions config.ini
View file
@@ -1,6 +1,6 @@
[InterVar]
buildver = hg19
# hg19 hg38
# hg19
inputfile = example/ex1.avinput
# the inputfile and the path example/ex1.avinput hg19_clinvar_20151201.avinput
# tab-delimited will be better for including the other information
Expand Down Expand Up @@ -57,9 +57,9 @@ annotate_variation = ./annotate_variation.pl
# annotate_variation of file location
database_locat = humandb
# the database location/dir from annnovar check if database file exists
database_names = refGene esp6500siv2_all 1000g2015aug avsnp147 dbnsfp33a clinvar_20170905 exac03 dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene
database_names = refGene esp6500siv2_all 1000g2015aug avsnp147 dbnsfp33a clinvar_20170905 gnomad_genome dbscsnv11 dbnsfp31a_interpro rmsk ensGene knownGene
# specify the database_names from ANNOVAR or UCSC
[Other]
current_version = Intervar_20180118
current_version = Intervar_20180827
# pipeline version
public_dev = https://github.com/WGLab/InterVar/releases

0 comments on commit a846dea

Please sign in to comment.