Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

VariantsToVCF - Table Codec

wukhanwukhan PakistanMember

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.

Tagged:

Issue · Github
by Sheila

Issue Number
1952
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi @wukhan, sorry for the late response. Those two tools aren't coordinated, so the table format expected by VariantsToVCF via the TableCodec is a bit different from what VariantsToTable outputs. We currently don't have documentation on what TableCodec requires (this tool is rarely used and has been neglected for a long time) so I can't tell you what it needs. I realize that's not ideal, but it sounds like you've figured out a solution anyway. Apologies for the inconvenience!

Answers

  • wukhanwukhan PakistanMember

    Hi,

    Dear GATK Community,

    If this post is missed, here it is once again.

    I converted csv to vcf by some linux commands tricks, but I am still curious to know the solution. This sort of question is novel at GATK community, and hopefully it will be discussed (TableCodec, TABLE feature etc.,)

    Thanks,

    Waqas.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Hi @wukhan, sorry for the late response. Those two tools aren't coordinated, so the table format expected by VariantsToVCF via the TableCodec is a bit different from what VariantsToTable outputs. We currently don't have documentation on what TableCodec requires (this tool is rarely used and has been neglected for a long time) so I can't tell you what it needs. I realize that's not ideal, but it sounds like you've figured out a solution anyway. Apologies for the inconvenience!

Sign In or Register to comment.