Hi,
Dear GATK Team,
I am converting a table file (generated from VariatnsToTable) to VCF by (VariatnsToVCF). My command is:
java -jar /home/wuk/software/GenomeAnalysisTK.jar -T VariantsToVCF -R /home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly38.fasta -o sg_in_234_nt4_new_hyp_gnomAD.vcf -V:TABLE sg_in_234_nt4_new_hyp_srt.TABLE
The command run fine but the output vcf file is empty.
The header part of input table file is:
HEADER CHROM POS ID REF ALT QUAL AC AF AN DP QD FS MQ Func.refGene ExonicFunc.refGene Gene.refGene GeneDetail.refGene AAChange.refGene SIFT_pred SIFT_score Polyphen2_HDIV_score Polyphen2_HDIV_pred LRT_score LRT_score.1 LRT_pred MutationTaster_pred MutationAssessor_score MutationAssessor_pred FATHMM_score FATHMM_pred PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_phred DANN_score fathmm.MKL_coding_score fathmm.MKL_coding_pred MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred integrated_fitCons_score integrated_confidence_value GERP.._RS phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_vertebrate phastCons20way_mammalian SiPhy_29way_logOdds esp6500siv2_all esp6500siv2_ea ExAC_ALL ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS X1000g2015aug_all MCAP REVEL ReMM clinvar_20161128 DEL.ETI.3.GT DEL.ETI.3.AD DEL.ETI.3.DP FR.RR DEL.ETI.3.GQ DEL.ETI.3.PL DEL.GIL.1.GT DEL.GIL.1.AD DEL.GIL.1.DP FR.RR.1 DEL.GIL.1.GQ DEL.GIL.1.PL DEL.JOE.GT DEL.JOE.AD DEL.JOE.DP FR.RR.2 DEL.JOE.GQ DEL.JOE.PL DEL.MAR.18.GT DEL.MAR.18.AD DEL.MAR.18.DP FR.RR.3 DEL.MAR.18.GQ DEL.MAR.18.PL SG_in_all SG_in_123_nt4 SG_in_234_nt1 SG_in_341_nt2 SG_in_412_nt3 ENSGID Gene.Name Adipose...Subcutaneous Adipose...Visceral..Omentum. Adrenal.Gland Artery...Aorta Artery...Coronary Artery...Tibial Bladder Brain...Amygdala Brain...Anterior.cingulate.cortex..BA24. Brain...Caudate..basal.ganglia. Brain...Cerebellar.Hemisphere Brain...Cerebellum Brain...Cortex Brain...Frontal.Cortex..BA9. Brain...Hippocampus Brain...Hypothalamus Brain...Nucleus.accumbens..basal.ganglia. Brain...Putamen..basal.ganglia. Brain...Spinal.cord..cervical.c.1. Brain...Substantia.nigra Breast...Mammary.Tissue Cells...EBV.transformed.lymphocytes Cells...Transformed.fibroblasts Cervix...Ectocervix Cervix...Endocervix Colon...Sigmoid Colon...Transverse Esophagus...Gastroesophageal.Junction Esophagus...Mucosa Esophagus...Muscularis Fallopian.Tube Heart...Atrial.Appendage Heart...Left.Ventricle Kidney...Cortex Liver Lung Minor.Salivary.Gland Muscle...Skeletal Nerve...Tibial Ovary Pancreas Pituitary Prostate Skin...Not.Sun.Exposed..Suprapubic. Skin...Sun.Exposed..Lower.leg. Small.Intestine...Terminal.Ileum Spleen Stomach Testis Thyroid Uterus Vagina Whole.Blood
chr1 11827316 rs55749208 T TG 1258.86 3 0.375 8 134 15.35 2.915 59.25 intronic 0 CLCN6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.563 0 T/T 32,0 32 A:0:0:C:0:0:G:0:0:T:3:34:N:0:0::: 99 0,102,1252 T/TG 21,16 37 A:0:0:C:0:0:G:0:0:T:1:43:N:0:0:+G:0:16 99 398,0,535 T/TG 11,19 30 A:0:0:C:0:0:G:0:0:T:0:32:N:0:0:+G:0:19 99 576,0,368 T/TG 3,12 15 A:0:0:C:0:0:G:1:0:T:2:20:N:0:0:+A:0:1 84 328,0,84 0 0 1 0 0 ENSG00000011021.17 CLCN6 9.132 6.543 8.069 6.235 6.653 7.582 7.954 8.334 12.06 8.468 14.43 15.45 13.24 14.36 9.121 13.94 8.502 7.009 10.1 9.69 8.733 7.619 5.341 8.387 12.16 8.766 6.543 8.315 4.103 7.799 8.747 5.625 4.174 6.824 4.312 9.778 5.059 3.466 13.38 12.81 3.502 14.87 9.382 5.686 6.351 8.659 8.304 6.063 15.84 11.08 11.29 7.418 1.663
I know there is something wrong in header part of input table file. What should be the header part of table file? or is there something else wrong?
Thanks,
Waqas.