Hello All,
I am working on Human exome project, where i would like to annotate variant file(VCF).
For this purpose i am using Cassandra, i have downloaded all required files and dependencies to there appropriate folder.
Ran Cassandra successfully and got output file, in which some of the fields are empty in every coordinates.
TMAF=. TAMR=. TASN=. TAFR=. TEUR=. RSID=. CD=. NA=. NC=. NE=. NF=. NG=. NH=. NI=. NJ=. NK=. NL=. NM=. MS=. CG=. AV=. AT=. EV=. ET=.
Example:
chr2 26426955 . C T 77.36 PASS OID=. OPOS=26426955 OREF=C OALT=T OMAPALT=T AO=17 DP=35 FAO=17 FDP=35 FR=. FRO=18 FSAF=3 FSAR=14 FSRF=11 FSRR=7 FWDB=0.0266816 FXX=0 HRUN=1 HS=. LEN=1 MLLD=72.2745 NR=. NS=. QD=8.84143 RBI=0.051232 REFB=0.00389769 REVB=-0.0437356 RO=18 SAF=3 SAR=14 SRF=11 SRR=7 SSEN=0 SSEP=0 SSSB=-0.444925 STB=0.756423 TYPE=snp VARB=-0.00587872 PU=. RFG=nonsynonymous_SNV GI=HADHA:NM_000182:exon12:c.G1196A: p.R399Q,,NONE(dist=NONE),NONE(dist=NONE),HADHA:uc002rgy.3:exon12:c.G1196A: p.R399Q,HADHA:uc010yks.2:exon11:c.G935A: p.R312Q,,ENSG00000084754:ENST00000380649:exon12:c.G1196A: p.R399Q, UCG=nonsynonymous_SNV ENS=nonsynonymous_SNV ENSGN=ENSG00000084754 MT=intergenic MTGN=. GN=HADHA TMAF=. TAMR=. TASN=. TAFR=. TEUR=. RSID=. CD=. NA=. NC=. NE=. NF=. NG=. NH=. NI=. NJ=. NK=. NL=. NM=. MS=. CG=. AV=. AT=. EV=. ET=. SF=Bifunctional_subunit. SD=Maternal_acute_fatty_liver_of_pregnancy_(AFLP)_[MIM:609016]:_Severe_maternal_illness_occurring_during_pregnancies_with_affected_fetuses._This_disease_is_associated_with_LCHAD_deficiency_and_characterized_by_sudden_unexplained_infant_death_or_hypoglycemia_and_abnormal_liver_enzymes_(Reye-like_syndrome)._Note=The_disease_is_caused_by_mutations_affecting_the_gene_represented_in_this_entry. SM=. SX=. ENN=. ENC=. CID=. CGENE=. CSTRAND=. CCDS=. CAA=. CCNT=. GT:GQ
P:FDP:RO:FRO:AO:FAO:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:76:35:35:18:18:17:17:14:3:11:7:14:3:11:7
Command:
java -jar /opt/installers/Cassandra_13.10.01/Cassandra.jar -t Annotate -i ../TSVC_variants_IonXpress_006.vcf -o TSVC_variants_IonXpress_006_OUT_Cassandra.vcf -n 15 --annovarPath /opt/installers/ANNOVAR_LATEST/annovar/ --annovarDB /opt/installers/ANNOVAR_LATEST/annovar/hg19_humandb_annovar/ --annotationSources /opt/installers/Cassandra_13.10.01/cassandraDataSources/DataSources/
Please give me suggestions.
I am working on Human exome project, where i would like to annotate variant file(VCF).
For this purpose i am using Cassandra, i have downloaded all required files and dependencies to there appropriate folder.
Ran Cassandra successfully and got output file, in which some of the fields are empty in every coordinates.
TMAF=. TAMR=. TASN=. TAFR=. TEUR=. RSID=. CD=. NA=. NC=. NE=. NF=. NG=. NH=. NI=. NJ=. NK=. NL=. NM=. MS=. CG=. AV=. AT=. EV=. ET=.
Example:
chr2 26426955 . C T 77.36 PASS OID=. OPOS=26426955 OREF=C OALT=T OMAPALT=T AO=17 DP=35 FAO=17 FDP=35 FR=. FRO=18 FSAF=3 FSAR=14 FSRF=11 FSRR=7 FWDB=0.0266816 FXX=0 HRUN=1 HS=. LEN=1 MLLD=72.2745 NR=. NS=. QD=8.84143 RBI=0.051232 REFB=0.00389769 REVB=-0.0437356 RO=18 SAF=3 SAR=14 SRF=11 SRR=7 SSEN=0 SSEP=0 SSSB=-0.444925 STB=0.756423 TYPE=snp VARB=-0.00587872 PU=. RFG=nonsynonymous_SNV GI=HADHA:NM_000182:exon12:c.G1196A: p.R399Q,,NONE(dist=NONE),NONE(dist=NONE),HADHA:uc002rgy.3:exon12:c.G1196A: p.R399Q,HADHA:uc010yks.2:exon11:c.G935A: p.R312Q,,ENSG00000084754:ENST00000380649:exon12:c.G1196A: p.R399Q, UCG=nonsynonymous_SNV ENS=nonsynonymous_SNV ENSGN=ENSG00000084754 MT=intergenic MTGN=. GN=HADHA TMAF=. TAMR=. TASN=. TAFR=. TEUR=. RSID=. CD=. NA=. NC=. NE=. NF=. NG=. NH=. NI=. NJ=. NK=. NL=. NM=. MS=. CG=. AV=. AT=. EV=. ET=. SF=Bifunctional_subunit. SD=Maternal_acute_fatty_liver_of_pregnancy_(AFLP)_[MIM:609016]:_Severe_maternal_illness_occurring_during_pregnancies_with_affected_fetuses._This_disease_is_associated_with_LCHAD_deficiency_and_characterized_by_sudden_unexplained_infant_death_or_hypoglycemia_and_abnormal_liver_enzymes_(Reye-like_syndrome)._Note=The_disease_is_caused_by_mutations_affecting_the_gene_represented_in_this_entry. SM=. SX=. ENN=. ENC=. CID=. CGENE=. CSTRAND=. CCDS=. CAA=. CCNT=. GT:GQ
P:FDP:RO:FRO:AO:FAO:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 0/1:76:35:35:18:18:17:17:14:3:11:7:14:3:11:7Command:
java -jar /opt/installers/Cassandra_13.10.01/Cassandra.jar -t Annotate -i ../TSVC_variants_IonXpress_006.vcf -o TSVC_variants_IonXpress_006_OUT_Cassandra.vcf -n 15 --annovarPath /opt/installers/ANNOVAR_LATEST/annovar/ --annovarDB /opt/installers/ANNOVAR_LATEST/annovar/hg19_humandb_annovar/ --annotationSources /opt/installers/Cassandra_13.10.01/cassandraDataSources/DataSources/
Please give me suggestions.