Mercurial > repos > iuc > gemini_lof_sieve

view test-data/gemini_de_novo_result.tabular @ 3:90021fffff70 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
author iuc
date Wed, 17 Oct 2018 13:27:38 -0400
parents be7ac09bc2fa
children
line wrap: on
line source

chrom	start	end	vcf_id	variant_id	anno_id	ref	alt	qual	filter	type	sub_type	call_rate	in_dbsnp	rs_ids	sv_cipos_start_left	sv_cipos_end_left	sv_cipos_start_right	sv_cipos_end_right	sv_length	sv_is_precise	sv_tool	sv_evidence_type	sv_event_id	sv_mate_id	sv_strand	in_omim	clinvar_sig	clinvar_disease_name	clinvar_dbsource	clinvar_dbsource_id	clinvar_origin	clinvar_dsdb	clinvar_dsdbid	clinvar_disease_acc	clinvar_in_locus_spec_db	clinvar_on_diag_assay	clinvar_causal_allele	pfam_domain	cyto_band	rmsk	in_cpg_island	in_segdup	is_conserved	gerp_bp_score	gerp_element_pval	num_hom_ref	num_het	num_hom_alt	num_unknown	aaf	hwe	inbreeding_coeff	pi	recomb_rate	gene	transcript	is_exonic	is_coding	is_splicing	is_lof	exon	codon_change	aa_change	aa_length	biotype	impact	impact_so	impact_severity	polyphen_pred	polyphen_score	sift_pred	sift_score	anc_allele	rms_bq	cigar	depth	strand_bias	rms_map_qual	in_hom_run	num_mapq_zero	num_alleles	num_reads_w_dels	haplotype_score	qual_depth	allele_count	allele_bal	in_hm2	in_hm3	is_somatic	somatic_score	in_esp	aaf_esp_ea	aaf_esp_aa	aaf_esp_all	exome_chip	in_1kg	aaf_1kg_amr	aaf_1kg_eas	aaf_1kg_sas	aaf_1kg_afr	aaf_1kg_eur	aaf_1kg_all	grc	gms_illumina	gms_solid	gms_iontorrent	in_cse	encode_tfbs	encode_dnaseI_cell_count	encode_dnaseI_cell_list	encode_consensus_gm12878	encode_consensus_h1hesc	encode_consensus_helas3	encode_consensus_hepg2	encode_consensus_huvec	encode_consensus_k562	vista_enhancers	cosmic_ids	info	cadd_raw	cadd_scaled	fitcons	in_exac	aaf_exac_all	aaf_adj_exac_all	aaf_adj_exac_afr	aaf_adj_exac_amr	aaf_adj_exac_eas	aaf_adj_exac_fin	aaf_adj_exac_nfe	aaf_adj_exac_oth	aaf_adj_exac_sas	exac_num_het	exac_num_hom_alt	exac_num_chroms	max_aaf_all	gts	gt_types	gt_phases	gt_depths	gt_ref_depths	gt_alt_depths	gt_quals	gt_copy_numbers	gt_phred_ll_homref	gt_phred_ll_het	gt_phred_ll_homalt	family_id	family_members	family_genotypes	samples	family_count
chr10	48003991	48003992	None	2	1	C	T	1047.86999512	None	snp	ts	1.0	1	rs142685947,rs3739968	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	1	None	3.10871e-42	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	1	0.3112	0.4573	0.3855	0.1241	0.5149	0.346645	grc_fix	73.3	40.3	92.8	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.553676	1	0.443	0.448537771896	0.288974151858	0.281426746944	0.543088975937	0.524984286612	0.478147713207	0.463529411765	0.418641164716	17495	15317	107302	0.543088975937	['C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T' 'C/T' 'C/T' 'C/T']	[1 1 3 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	C/C,C/C,C/T	2_kid	2
chr10	48004991	48004992	None	3	1	C	T	1047.86999512	None	snp	ts	1.0	0	None	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q11.22	None	0	1	0	None	None	2	6	1	0	0.444444444444	0.29371811258	-0.35	0.522875816993	1.718591	ASAH2C	ENST00000420079	1	1	0	0	exon_10_48003968_48004056	tGt/tAt	C540Y	610	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	165	None	20.9400005341	0	0	8	0.0	4.382999897	9.52999973297	4	None	None	None	None	None	0	None	None	None	0	0	None	None	None	None	None	None	grc_fix	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.061011	0	None	None	None	None	None	None	None	None	None	None	None	None	-1.0	['C/T' 'C/T' 'C/T' 'C/T' 'C/T' 'T/T' 'C/C' 'C/C' 'C/T']	[1 1 1 1 1 3 0 0 1]	[False False False False False False False False False]	[38 29 23 38 29 23 38 29 23]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 23 37 29 23]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	C/C,C/C,C/T	3_kid	2
chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	G/G,G/G,G/A	1_kid	2
chr10	135336655	135336656	None	4	1	G	A	38.3400001526	None	snp	ts	1.0	1	rs6537611	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	0	None	None	4	5	0	0	0.277777777778	0.248563248239	-0.384615384615	0.424836601307	0.43264	SPRN	ENST00000541506	0	0	0	0				151	protein_coding	intron_variant	intron_variant	LOW	None	None	None	None	None	None	None	2	None	37.0	4	0	4	0.0	0.0	19.1700000763	4	None	None	None	None	None	0	None	None	None	0	1	0.9957	1	1	0.9297	1	0.980831	None	None	None	None	0	None	None	None	R	R	R	R	unknown	R	None	None	None	None	None	0.056701	0	None	None	None	None	None	None	None	None	None	None	None	None	1.0	['G/G' 'G/G' 'G/A' 'G/G' 'G/G' 'G/A' 'G/A' 'G/A' 'G/A']	[0 0 1 0 0 1 1 1 1]	[False False False False False False False False False]	[38 29 24 38 29 24 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 24 37 29 24 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	G/G,G/G,G/A	2_kid	2
chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	3
chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	3	3_dad(3_dad;unaffected),3_mom(3_mom;unaffected),3_kid(3_kid;affected)	T/T,T/T,T/C	3_kid	3
chr10	135369531	135369532	None	5	6	T	C	122.620002747	None	snp	ts	1.0	1	rs3747881,rs386585367	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10q26.3	None	0	0	1	None	3.86096e-59	6	3	0	0	0.166666666667	0.548506235587	-0.2	0.294117647059	0.022013	SYCE1	ENST00000368517	1	1	0	0	exon_10_135369485_135369551	aAg/aGg	K147R	282	protein_coding	missense_variant	missense_variant	MED	None	None	None	None	None	None	None	239	None	36.0200004578	2	0	8	0.0	5.71409988403	2.30999994278	2	None	None	None	None	None	1	0.0938372093023	0.163867453473	0.117561125634	1	1	0.1844	0.2698	0.2188	0.1997	0.1093	0.197284	None	None	None	None	0	None	None	None	R	R	R	R	R	R	None	None	None	None	None	0.487112	1	0.134	0.134286610119	0.184985563041	0.164938655607	0.256026889198	0.122313048744	0.0919761054243	0.113686534216	0.194096927001	13825	1225	121196	0.2698	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/C']	[0 0 1 0 0 1 0 0 1]	[False False False False False False False False False]	[38 29 22 38 29 21 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 22 37 29 21 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	2	2_dad(2_dad;unaffected),2_mom(2_mom;unaffected),2_kid(2_kid;affected)	T/T,T/T,T/C	2_kid	3
chr10	1142207	1142208	None	1	4	T	C	3404.30004883	None	snp	ts	1.0	1	rs10794716	None	None	None	None	None	1	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	None	chr10p15.3	None	0	0	0	None	None	7	1	1	0	0.166666666667	0.0718606383197	0.6	0.294117647059	0.200924	WDR37	ENST00000381329	1	1	0	1	exon_10_1142110_1142566	Tga/Cga	*250R	249	protein_coding	stop_lost	stop_lost	HIGH	None	None	None	None	None	None	None	122	None	36.0	0	0	8	0.0	2.67470002174	27.8999996185	8	None	None	None	None	None	1	0.999534883721	0.975034044485	0.991234814701	0	1	0.9942	1	1	0.9561	1	0.98762	None	None	None	None	0	None	2	Osteobl;Progfib	T	T	T	T	T	T	None	None	None	None	None	0.156188	1	0.997	0.997067786838	0.970305592927	0.998358956642	1	1	0.999595432887	0.998898678414	1	346	60354	121410	1.0	['T/T' 'T/T' 'T/C' 'T/T' 'T/T' 'T/T' 'T/T' 'T/T' 'C/C']	[0 0 1 0 0 0 0 0 3]	[False False False False False False False False False]	[38 29 23 38 29 22 38 29 24]	[1 0 0 1 0 0 1 0 0]	[37 29 23 37 29 22 37 29 24]	[ 87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939  87.16000366  78.19999695  66.13999939]	None	[940 899 729 940 899 729 940 899 729]	[87 78 66 87 78 66 87 78 66]	[0 0 0 0 0 0 0 0 0]	1	1_dad(1_dad;unaffected),1_mom(1_mom;unaffected),1_kid(1_kid;affected)	T/T,T/T,T/C	1_kid	1