Hello,
I want to annotate my file through gatk 3.8 but I get this error:
MESSAGE: Your input file has a malformed header: there are not enough columns present in the header line: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AERMQNK-paris-8400326-P6-recipient BEGHUSZ-paris-CIN130255-P5-donor BNAGPIP-paris-SCE240246-P1-donor DKFEYNF-paris-9402755-P24-recipient DUWPYOX-paris-LAP201156-P2-donor ENERRIA-paris-7406853-P13-donor FSCDYAD-paris-08404250-P18-recipient GZISOJR-paris-7400781-P16-donor HDXJQEQ-paris-BOU231086-P8-recipient HPPXKJR-paris-DAS070568-P11-recipient IBMRISR-paris-1012026425-P14-donor JBQRXUU-paris-BAL040960-P4-donor JGYNLLJ-paris-9406986-P22-donor JOJLUPS-paris-CIN020578-P5-recipient KXQMHUU-paris-PAQ030369-P10-donor MFQDFBY-paris-6405545-P19-donor MMGEWHT-paris-7400697-P16-recipient MVDUSTB-paris-BAR131257-P10-recipient MVTISRC-paris-761011046144-P14-recipient NEYXWDZ-paris-RIZ120484-P9-recipient NFAMZIJ-paris-09406539-P22-recipient OENIGXI-paris-6405485-P17-donor ONDAMJK-paris-SCE260544-P1-recipient PAIFUYN-paris-JEA110683-P7-donor QGGDOUC-paris-GIL090756-P3-donor QNIODCU-paris-06405141-P19-recipient RGFUJSJ-paris-7405431-P15-donor RPUJEMI-paris-JEA050373-P7-recipient RZBCDKZ-paris-06400985-P15-recipient SNDXLDU-paris-06404984-P17-recipient TRPLSFT-paris-7401924-P13-recipient UFVLBVS-paris-GIL160150-P3-recipient VOCSMLM-paris-DEL240879-P2-recipient WKCQCMA-paris-9402754-P24-donor WKXMWKI-paris-8404252-P18-donor XUPTJWH-paris-RIZ310548-P9-donor YPOYSQD-paris-DAC250146-P11-donor YYMSZHP-paris-DEM300679-P6-donor ZCRWXBD-paris-BOU280575-P8-donor ZGAQHAH-paris-BAL251159-P4-recipient
after research, I don't see what can generate the program.
Header of my vcf:
##fileformat=VCFv4.1
##Goby=development (20150227145140)
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##INFO=
##source_20150426.1=vcf-annotate(r797) -a output-21711.tsv.gz -d /scratchLocal/gobyweb/tmp/421024.1.rascals.q/attributes.lst -c CHROM,FROM,TO,INFO/VariantEffectPrediction
##INFO=
##INFO=
##source_20150426.2=vcf-annotate(r797) -a /scratchLocal/gobyweb/ARTIFACT_REPOSITORY-dev/artifacts/ENSEMBL_ANNOTATIONS/ANNOTATIONS/2.1.3/HOMO_SAPIENS/1000GENOMES/37/ref-start-end-gene-hgnc-sorted.tsv.gz -d /scratchLocal/gobyweb/tmp/421024.1.rascals.q/attributes.lst -c CHROM,FROM,TO,INFO/GENE,INFO/GENE_NAME
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AERMQNK-paris-8400326-P6-recipient BEGHUSZ-paris-CIN130255-P5-donor BNAGPIP-paris-SCE240246-P1-donor DKFEYNF-paris-9402755-P24-recipient DUWPYOX-paris-LAP201156-P2-donor ENERRIA-paris-7406853-P13-donor FSCDYAD-paris-08404250-P18-recipient GZISOJR-paris-7400781-P16-donor HDXJQEQ-paris-BOU231086-P8-recipient HPPXKJR-paris-DAS070568-P11-recipient IBMRISR-paris-1012026425-P14-donor JBQRXUU-paris-BAL040960-P4-donor JGYNLLJ-paris-9406986-P22-donor JOJLUPS-paris-CIN020578-P5-recipient KXQMHUU-paris-PAQ030369-P10-donor MFQDFBY-paris-6405545-P19-donor MMGEWHT-paris-7400697-P16-recipient MVDUSTB-paris-BAR131257-P10-recipient MVTISRC-paris-761011046144-P14-recipient NEYXWDZ-paris-RIZ120484-P9-recipient NFAMZIJ-paris-09406539-P22-recipient OENIGXI-paris-6405485-P17-donor ONDAMJK-paris-SCE260544-P1-recipient PAIFUYN-paris-JEA110683-P7-donor QGGDOUC-paris-GIL090756-P3-donor QNIODCU-paris-06405141-P19-recipient RGFUJSJ-paris-7405431-P15-donor RPUJEMI-paris-JEA050373-P7-recipient RZBCDKZ-paris-06400985-P15-recipient SNDXLDU-paris-06404984-P17-recipient TRPLSFT-paris-7401924-P13-recipient UFVLBVS-paris-GIL160150-P3-recipient VOCSMLM-paris-DEL240879-P2-recipient WKCQCMA-paris-9402754-P24-donor WKXMWKI-paris-8404252-P18-donor XUPTJWH-paris-RIZ310548-P9-donor YPOYSQD-paris-DAC250146-P11-donor YYMSZHP-paris-DEM300679-P6-donor ZCRWXBD-paris-BOU280575-P8-donor ZGAQHAH-paris-BAL251159-P4-recipient
1 721427 . C . . . BIOMART_COORDS=1:721427:721427;GENE=ENSG00000230021,ENSG00000237491 GT:BC:GB:FB:Zygosity 0/0:C=187:187:0:homozygous 0/0:C=202:202:2:homozygous 0/0:C=157:157:0:homozygous 0/0:C=153:153:0:homozygous 0/0:C=196:196:0:homozygous 0/0:C=111:111:0:homozygous 0/0:C=176:176:0:homozygous 0/0:C=73:73:0:homozygous 0/0:C=195:195:0:homozygous 0/0:C=199:199:0:homozygous 0/0:C=78:78:0:homozygous 0/0:C=243:243:0:homozygous 0/0:C=65:65:0:homozygous 0/0:C=189:189:0:homozygous 0/0:C=166:166:0:homozygous 0/0:C=245:245:2:homozygous 0/0:C=60:60:0:homozygous 0/0:C=224:224:0:homozygous 0/0:C=84:84:0:homozygous 0/0:C=138:138:0:homozygous 0/0:C=156:156:0:homozygous 0/0:C=84:84:0:homozygous 0/0:C=211:211:0:homozygous 0/0:C=234:234:0:homozygous 0/0:C=247:247:0:homozygous 0/0:C=187:187:0:homozygous 0/0:C=124:124:0:homozygous 0/0:C=201:201:0:homozygous 0/0:C=155:155:0:homozygous 0/0:C=168:168:0:homozygous 0/0:C=99:99:0:homozygous 0/0:C=179:179:0:homozygous 0/0:C=209:209:2:homozygous 0/0:C=91:91:0:homozygous 0/0:C=189:189:0:homozygous 0/0:C=206:206:0:homozygous 0/0:C=167:167:2:homozygous 0/0:C=159:159:0:homozygous 0/0:C=220:220:0:homozygous 0/0:C=222:222:0:homozygous
Thank you in advance.
I want to annotate my file through gatk 3.8 but I get this error:
MESSAGE: Your input file has a malformed header: there are not enough columns present in the header line: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AERMQNK-paris-8400326-P6-recipient BEGHUSZ-paris-CIN130255-P5-donor BNAGPIP-paris-SCE240246-P1-donor DKFEYNF-paris-9402755-P24-recipient DUWPYOX-paris-LAP201156-P2-donor ENERRIA-paris-7406853-P13-donor FSCDYAD-paris-08404250-P18-recipient GZISOJR-paris-7400781-P16-donor HDXJQEQ-paris-BOU231086-P8-recipient HPPXKJR-paris-DAS070568-P11-recipient IBMRISR-paris-1012026425-P14-donor JBQRXUU-paris-BAL040960-P4-donor JGYNLLJ-paris-9406986-P22-donor JOJLUPS-paris-CIN020578-P5-recipient KXQMHUU-paris-PAQ030369-P10-donor MFQDFBY-paris-6405545-P19-donor MMGEWHT-paris-7400697-P16-recipient MVDUSTB-paris-BAR131257-P10-recipient MVTISRC-paris-761011046144-P14-recipient NEYXWDZ-paris-RIZ120484-P9-recipient NFAMZIJ-paris-09406539-P22-recipient OENIGXI-paris-6405485-P17-donor ONDAMJK-paris-SCE260544-P1-recipient PAIFUYN-paris-JEA110683-P7-donor QGGDOUC-paris-GIL090756-P3-donor QNIODCU-paris-06405141-P19-recipient RGFUJSJ-paris-7405431-P15-donor RPUJEMI-paris-JEA050373-P7-recipient RZBCDKZ-paris-06400985-P15-recipient SNDXLDU-paris-06404984-P17-recipient TRPLSFT-paris-7401924-P13-recipient UFVLBVS-paris-GIL160150-P3-recipient VOCSMLM-paris-DEL240879-P2-recipient WKCQCMA-paris-9402754-P24-donor WKXMWKI-paris-8404252-P18-donor XUPTJWH-paris-RIZ310548-P9-donor YPOYSQD-paris-DAC250146-P11-donor YYMSZHP-paris-DEM300679-P6-donor ZCRWXBD-paris-BOU280575-P8-donor ZGAQHAH-paris-BAL251159-P4-recipient
after research, I don't see what can generate the program.
Header of my vcf:
##fileformat=VCFv4.1
##Goby=development (20150227145140)
##INFO=
##INFO=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##INFO=
##source_20150426.1=vcf-annotate(r797) -a output-21711.tsv.gz -d /scratchLocal/gobyweb/tmp/421024.1.rascals.q/attributes.lst -c CHROM,FROM,TO,INFO/VariantEffectPrediction
##INFO=
##INFO=
##source_20150426.2=vcf-annotate(r797) -a /scratchLocal/gobyweb/ARTIFACT_REPOSITORY-dev/artifacts/ENSEMBL_ANNOTATIONS/ANNOTATIONS/2.1.3/HOMO_SAPIENS/1000GENOMES/37/ref-start-end-gene-hgnc-sorted.tsv.gz -d /scratchLocal/gobyweb/tmp/421024.1.rascals.q/attributes.lst -c CHROM,FROM,TO,INFO/GENE,INFO/GENE_NAME
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AERMQNK-paris-8400326-P6-recipient BEGHUSZ-paris-CIN130255-P5-donor BNAGPIP-paris-SCE240246-P1-donor DKFEYNF-paris-9402755-P24-recipient DUWPYOX-paris-LAP201156-P2-donor ENERRIA-paris-7406853-P13-donor FSCDYAD-paris-08404250-P18-recipient GZISOJR-paris-7400781-P16-donor HDXJQEQ-paris-BOU231086-P8-recipient HPPXKJR-paris-DAS070568-P11-recipient IBMRISR-paris-1012026425-P14-donor JBQRXUU-paris-BAL040960-P4-donor JGYNLLJ-paris-9406986-P22-donor JOJLUPS-paris-CIN020578-P5-recipient KXQMHUU-paris-PAQ030369-P10-donor MFQDFBY-paris-6405545-P19-donor MMGEWHT-paris-7400697-P16-recipient MVDUSTB-paris-BAR131257-P10-recipient MVTISRC-paris-761011046144-P14-recipient NEYXWDZ-paris-RIZ120484-P9-recipient NFAMZIJ-paris-09406539-P22-recipient OENIGXI-paris-6405485-P17-donor ONDAMJK-paris-SCE260544-P1-recipient PAIFUYN-paris-JEA110683-P7-donor QGGDOUC-paris-GIL090756-P3-donor QNIODCU-paris-06405141-P19-recipient RGFUJSJ-paris-7405431-P15-donor RPUJEMI-paris-JEA050373-P7-recipient RZBCDKZ-paris-06400985-P15-recipient SNDXLDU-paris-06404984-P17-recipient TRPLSFT-paris-7401924-P13-recipient UFVLBVS-paris-GIL160150-P3-recipient VOCSMLM-paris-DEL240879-P2-recipient WKCQCMA-paris-9402754-P24-donor WKXMWKI-paris-8404252-P18-donor XUPTJWH-paris-RIZ310548-P9-donor YPOYSQD-paris-DAC250146-P11-donor YYMSZHP-paris-DEM300679-P6-donor ZCRWXBD-paris-BOU280575-P8-donor ZGAQHAH-paris-BAL251159-P4-recipient
1 721427 . C . . . BIOMART_COORDS=1:721427:721427;GENE=ENSG00000230021,ENSG00000237491 GT:BC:GB:FB:Zygosity 0/0:C=187:187:0:homozygous 0/0:C=202:202:2:homozygous 0/0:C=157:157:0:homozygous 0/0:C=153:153:0:homozygous 0/0:C=196:196:0:homozygous 0/0:C=111:111:0:homozygous 0/0:C=176:176:0:homozygous 0/0:C=73:73:0:homozygous 0/0:C=195:195:0:homozygous 0/0:C=199:199:0:homozygous 0/0:C=78:78:0:homozygous 0/0:C=243:243:0:homozygous 0/0:C=65:65:0:homozygous 0/0:C=189:189:0:homozygous 0/0:C=166:166:0:homozygous 0/0:C=245:245:2:homozygous 0/0:C=60:60:0:homozygous 0/0:C=224:224:0:homozygous 0/0:C=84:84:0:homozygous 0/0:C=138:138:0:homozygous 0/0:C=156:156:0:homozygous 0/0:C=84:84:0:homozygous 0/0:C=211:211:0:homozygous 0/0:C=234:234:0:homozygous 0/0:C=247:247:0:homozygous 0/0:C=187:187:0:homozygous 0/0:C=124:124:0:homozygous 0/0:C=201:201:0:homozygous 0/0:C=155:155:0:homozygous 0/0:C=168:168:0:homozygous 0/0:C=99:99:0:homozygous 0/0:C=179:179:0:homozygous 0/0:C=209:209:2:homozygous 0/0:C=91:91:0:homozygous 0/0:C=189:189:0:homozygous 0/0:C=206:206:0:homozygous 0/0:C=167:167:2:homozygous 0/0:C=159:159:0:homozygous 0/0:C=220:220:0:homozygous 0/0:C=222:222:0:homozygous
Thank you in advance.