Custom annotation issue

[omerfarukgerdan]

There is a problem with annotating files when the command run such as:

java -Xmx10g -jar SnpSift.jar annotate custom_clinvar.vcf test.vcf > test.custom_clinvar_annotated.vcf

custom_clinvar.vcf:

CHROM POS ID REF ALT QUAL FILTER INFO

1 985955 rs199476396 G C . . RS=199476396;RSPOS=985955;dbSNPBuildID=136;SSR=0;SAO=1;VP=0x050260000a01000002110100;GENEINFO=AGRN:375790;WGT=1;VC=SNV;PM;S3D;NSM;REF;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.985955G>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=103320.0001;CLNSIG=5;CLNDSDB=GeneReviews:MedGen:OMIM:Orphanet;CLNDSDBID=NBK1168:C1850792:254300:590;CLNDBN=Myasthenia\x2c_limb-girdle\x2c_familial;CLNACC=RCV000019902.1
1 1959075 . A C . . SSR=0;SAO=1;VP=0x050260000a01000002110111;GENEINFO=GABRD:2563;WGT=1;VC=SNV;PM;S3D;NSM;REF;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C1858675;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1
1 1959075 . A CG . . SSR=0;SAO=1;VP=0x050260000a01000002110100;GENEINFO=GABRD:2563;WGT=1;VC=SNV;PM;S3D;NSM;REF;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C1858675;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1

test.vcf:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT M_11_1435 M_11_1436 M_11_1437 M_11_1438

1 985955 . G CC 59.56 PASS . GT:AD:DP:GQ:PL 0/0:12,119:132:3:0,3,28 1/1:2,106:108:6.01:59,6,0 ./. 1/1:6,63:69:3.01:39,3,0
1 985955 rs199476396 G C 59.56 PASS . GT:AD:DP:GQ:PL 0/0:12,119:132:3:0,3,28 1/1:2,106:108:6.01:59,6,0 ./. 1/1:6,63:69:3.01:39,3,0
1 1959075 . A C 57.47 PASS . GT:AD:DP:GQ:PL 0/0:12,117:129:6.01:0,6,55 1/1:2,102:104:6.01:59,6,0 ./. 1/1:4,61:65:3.01:39,3,0
1 1959075 . A CG 197.52 PASS . GT:AD:DP:GQ:PL 0/1:9,235:245:99:174,0,118 1/1:1,199:201:6.01:59,6,0 ./. ./.

test.custom_clinvar_annotated.vcf:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT M_11_1435 M_11_1436 M_11_1437 M_11_1438

1 985955 . G CC 59.56 PASS . GT:AD:DP:GQ:PL 0/0:12,119:132:3:0,3,28 1/1:2,106:108:6.01:59,6,0 ./. 1/1:6,63:69:3.01:39,3,0
1 985955 rs199476396 G C 59.56 PASS . GT:AD:DP:GQ:PL 0/0:12,119:132:3:0,3,28 1/1:2,106:108:6.01:59,6,0 ./. 1/1:6,63:69:3.01:39,3,0
1 1959075 . A C 57.47 PASS SSR=0;SAO=1;VP=0x050260000a01000002110111;GENEINFO=GABRD:2563;WGT=1;VC=SNV;PM;S3D;NSM;REF;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C1858675;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1 GT:AD:DP:GQ:PL 0/0:12,117:129:6.01:0,6,55 1/1:2,102:104:6.01:59,6,0 ./. 1/1:4,61:65:3.01:39,3,0
1 1959075 . A CG 197.52 PASS SSR=0;SAO=1;VP=0x050260000a01000002110100;GENEINFO=GABRD:2563;WGT=1;VC=SNV;PM;S3D;NSM;REF;OTHERKG;LSD;OM;CLNALLE=1;CLNHGVS=NC_000001.10:g.1959075A>C;CLNSRC=OMIM_Allelic_Variant;CLNORIGIN=1;CLNSRCID=137163.0001;CLNSIG=255;CLNDSDB=MedGen;CLNDSDBID=C1858675;CLNDBN=Generalized_epilepsy_with_febrile_seizures_plus_type_5;CLNACC=RCV000017598.1 GT:AD:DP:GQ:PL 0/1:9,235:245:99:174,0,118 1/1:1,199:201:6.01:59,6,0 ./. ./.

When there are two types of snp/indel at same position, snpEff annotates only the first line but not the second.