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
