Understanding VerifyBamID output

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Expected Output from verifyBamID

This section explains the expected output from verifyBamID software. See VerifyBamID output documentation for more details.

There will be four types of files produced by verifyBamID

  • *.selfSM : Main output file containing the contamination estimate. If you are only interested in checking sample contamination, check the 'FREEMIX' column for genotype-free estimate of contamination, and 'CHIPMIX' column for contamination estimates with external genotypes (if provided)
  • *.selfRG : Same output to .*selfRG, but separated by readGroup (which might be helpful for library-level examination)
  • *.depthSM : The depth distribution of reads covering the marker position of the input VCF, across all readGroups.
  • *.depthRG : : The depth distribution of reads covering the marker position of the input VCF, per readGroups.

VerifyBamID Tutorial Output

The VerifyBamID output from the GotCloud Tutorial looks like this:

HG00096.genoCheck.depthRG

#RG	DEPTH	#SNPs	%SNPs	%CUMUL
SRR062634	20	0	0.00000	0.00000
SRR062634	19	0	0.00000	0.00000
SRR062634	18	0	0.00000	0.00000
SRR062634	17	0	0.00000	0.00000
SRR062634	16	0	0.00000	0.00000
SRR062634	15	0	0.00000	0.00000
SRR062634	14	0	0.00000	0.00000
SRR062634	13	0	0.00000	0.00000
SRR062634	12	0	0.00000	0.00000
SRR062634	11	0	0.00000	0.00000
SRR062634	10	0	0.00000	0.00000
SRR062634	9	0	0.00000	0.00000
SRR062634	8	0	0.00000	0.00000
SRR062634	7	0	0.00000	0.00000
SRR062634	6	0	0.00000	0.00000
SRR062634	5	1	0.00003	0.00003
SRR062634	4	1	0.00003	0.00006
SRR062634	3	9	0.00025	0.00030
SRR062634	2	22	0.00061	0.00091
SRR062634	1	62	0.00171	0.00262
SRR062634	0	36203	0.99738	1.00000
SRR062635	20	0	0.00000	0.00000
SRR062635	19	0	0.00000	0.00000
SRR062635	18	0	0.00000	0.00000
SRR062635	17	0	0.00000	0.00000
SRR062635	16	0	0.00000	0.00000
SRR062635	15	0	0.00000	0.00000
SRR062635	14	0	0.00000	0.00000
SRR062635	13	0	0.00000	0.00000
SRR062635	12	0	0.00000	0.00000
SRR062635	11	0	0.00000	0.00000
SRR062635	10	0	0.00000	0.00000
SRR062635	9	0	0.00000	0.00000
SRR062635	8	0	0.00000	0.00000
SRR062635	7	0	0.00000	0.00000
SRR062635	6	0	0.00000	0.00000
SRR062635	5	0	0.00000	0.00000
SRR062635	4	0	0.00000	0.00000
SRR062635	3	4	0.00011	0.00011
SRR062635	2	14	0.00039	0.00050
SRR062635	1	65	0.00179	0.00229
SRR062635	0	36215	0.99771	1.00000
SRR062641	20	0	0.00000	0.00000
SRR062641	19	0	0.00000	0.00000
SRR062641	18	0	0.00000	0.00000
SRR062641	17	0	0.00000	0.00000
SRR062641	16	0	0.00000	0.00000
SRR062641	15	0	0.00000	0.00000
SRR062641	14	0	0.00000	0.00000
SRR062641	13	0	0.00000	0.00000
SRR062641	12	0	0.00000	0.00000
SRR062641	11	0	0.00000	0.00000
SRR062641	10	0	0.00000	0.00000
SRR062641	9	0	0.00000	0.00000
SRR062641	8	0	0.00000	0.00000
SRR062641	7	0	0.00000	0.00000
SRR062641	6	0	0.00000	0.00000
SRR062641	5	1	0.00003	0.00003
SRR062641	4	3	0.00008	0.00011
SRR062641	3	8	0.00022	0.00033
SRR062641	2	23	0.00063	0.00096
SRR062641	1	58	0.00160	0.00256
SRR062641	0	36205	0.99744	1.00000


HG00096.genoCheck.depthSM

#RG	DEPTH	#SNPs	%SNPs	%CUMUL
ALL	20	0	0.00000	0.00000
ALL	19	0	0.00000	0.00000
ALL	18	0	0.00000	0.00000
ALL	17	0	0.00000	0.00000
ALL	16	0	0.00000	0.00000
ALL	15	0	0.00000	0.00000
ALL	14	0	0.00000	0.00000
ALL	13	0	0.00000	0.00000
ALL	12	0	0.00000	0.00000
ALL	11	0	0.00000	0.00000
ALL	10	0	0.00000	0.00000
ALL	9	0	0.00000	0.00000
ALL	8	2	0.00006	0.00006
ALL	7	2	0.00006	0.00011
ALL	6	7	0.00019	0.00030
ALL	5	10	0.00028	0.00058
ALL	4	17	0.00047	0.00105
ALL	3	34	0.00094	0.00198
ALL	2	31	0.00085	0.00284
ALL	1	38	0.00105	0.00388
ALL	0	36157	0.99612	1.00000


HG00096.genoCheck.selfRG

#SEQ_ID	RG	CHIP_ID	#SNPS	#READS	AVG_DP	FREEMIX	FREELK1	FREELK0	FREE_RH	FREE_RA	CHIPMIX	CHIPLK1	CHIPLK0	CHIP_RH	CHIP_RA	DPREF	RDPHET	RDPALT
HG00096	SRR062634	NA	36298	142	0.00	0.00000	40.76	40.76	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
HG00096	SRR062635	NA	36298	105	0.00	0.00000	38.05	38.05	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
HG00096	SRR062641	NA	36298	145	0.00	0.00000	43.96	43.96	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA


HG00096.genoCheck.selfSM

#SEQ_ID	RG	CHIP_ID	#SNPS	#READS	AVG_DP	FREEMIX	FREELK1	FREELK0	FREE_RH	FREE_RA	CHIPMIX	CHIPLK1	CHIPLK0	CHIP_RH	CHIP_RA	DPREF	RDPHET	RDPALT
HG00096	ALL	NA	36298	392	0.01	0.00000	86.22	86.22	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA


HG00100.genoCheck.depthRG

#RG	DEPTH	#SNPs	%SNPs	%CUMUL
ERR013140	20	0	0.00000	0.00000
ERR013140	19	0	0.00000	0.00000
ERR013140	18	0	0.00000	0.00000
ERR013140	17	0	0.00000	0.00000
ERR013140	16	0	0.00000	0.00000
ERR013140	15	0	0.00000	0.00000
ERR013140	14	0	0.00000	0.00000
ERR013140	13	0	0.00000	0.00000
ERR013140	12	0	0.00000	0.00000
ERR013140	11	0	0.00000	0.00000
ERR013140	10	0	0.00000	0.00000
ERR013140	9	0	0.00000	0.00000
ERR013140	8	0	0.00000	0.00000
ERR013140	7	0	0.00000	0.00000
ERR013140	6	0	0.00000	0.00000
ERR013140	5	1	0.00003	0.00003
ERR013140	4	2	0.00006	0.00008
ERR013140	3	3	0.00008	0.00017
ERR013140	2	23	0.00063	0.00080
ERR013140	1	44	0.00121	0.00201
ERR013140	0	36225	0.99799	1.00000
ERR016352	20	0	0.00000	0.00000
ERR016352	19	0	0.00000	0.00000
ERR016352	18	0	0.00000	0.00000
ERR016352	17	0	0.00000	0.00000
ERR016352	16	0	0.00000	0.00000
ERR016352	15	0	0.00000	0.00000
ERR016352	14	0	0.00000	0.00000
ERR016352	13	0	0.00000	0.00000
ERR016352	12	0	0.00000	0.00000
ERR016352	11	0	0.00000	0.00000
ERR016352	10	0	0.00000	0.00000
ERR016352	9	0	0.00000	0.00000
ERR016352	8	0	0.00000	0.00000
ERR016352	7	0	0.00000	0.00000
ERR016352	6	0	0.00000	0.00000
ERR016352	5	0	0.00000	0.00000
ERR016352	4	0	0.00000	0.00000
ERR016352	3	0	0.00000	0.00000
ERR016352	2	4	0.00011	0.00011
ERR016352	1	22	0.00061	0.00072
ERR016352	0	36272	0.99928	1.00000


HG00100.genoCheck.depthSM

#RG	DEPTH	#SNPs	%SNPs	%CUMUL
ALL	20	0	0.00000	0.00000
ALL	19	0	0.00000	0.00000
ALL	18	0	0.00000	0.00000
ALL	17	0	0.00000	0.00000
ALL	16	0	0.00000	0.00000
ALL	15	0	0.00000	0.00000
ALL	14	0	0.00000	0.00000
ALL	13	0	0.00000	0.00000
ALL	12	0	0.00000	0.00000
ALL	11	0	0.00000	0.00000
ALL	10	0	0.00000	0.00000
ALL	9	0	0.00000	0.00000
ALL	8	0	0.00000	0.00000
ALL	7	0	0.00000	0.00000
ALL	6	2	0.00006	0.00006
ALL	5	0	0.00000	0.00006
ALL	4	1	0.00003	0.00008
ALL	3	9	0.00025	0.00033
ALL	2	28	0.00077	0.00110
ALL	1	43	0.00118	0.00229
ALL	0	36215	0.99771	1.00000


HG00100.genoCheck.selfSM

#SEQ_ID	RG	CHIP_ID	#SNPS	#READS	AVG_DP	FREEMIX	FREELK1	FREELK0	FREE_RH	FREE_RA	CHIPMIX	CHIPLK1	CHIPLK0	CHIP_RH	CHIP_RA	DPREF	RDPHET	RDPALT
HG00100	ALL	NA	36298	142	0.00	0.49991	59.51	60.55	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA


HG00100.genoCheck.selfRG

#SEQ_ID	RG	CHIP_ID	#SNPS	#READS	AVG_DP	FREEMIX	FREELK1	FREELK0	FREE_RH	FREE_RA	CHIPMIX	CHIPLK1	CHIPLK0	CHIP_RH	CHIP_RA	DPREF	RDPHET	RDPALT
HG00100	ERR013140	NA	36298	112	0.00	0.49995	48.17	49.67	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA
HG00100	ERR016352	NA	36298	30	0.00	0.49995	12.52	12.61	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA