tab_to_vcf.py,

[ghost]

Hi,

Dear vcf-flow Team,

I am using tab_to_vcf.py to convert my tab-delimited variants to vcf format. My command is:

python tab_to_vcf.py /home/wuk/Working/vcf_samples/waqas.TABLE /home/wuk/Working/vcf_samples/waqas.vcf /home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly38.fasta --info-fields AC:ac,AF:af

I came up with an error:

Traceback (most recent call last):
File "tab_to_vcf.py", line 183, in
tab_to_vcf(args.input_file, args.output_file, args.reference_file, convert_iupac=args.convert_iupac, info_fields=INFO_FIELDS)
File "tab_to_vcf.py", line 139, in tab_to_vcf
args[POSITION_INDEX] = int(args[POSITION_INDEX])
ValueError: invalid literal for int() with base 10: '.'

My tab variant file looks like this:

CHROM	POS	ID	REF	ALT	QUAL	FILTER	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	PASS	3	0.375	8	134	15.35	2.915	59.25	intronic	0CLCN6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	000	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	000	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

Is this a bug, or my tab file has some issues,????

Looking forward for your kind response,

Thanks,

Waqas.