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Revision as of 23:12, 24 February 2013
, 23:12, 24 February 2013Created page with '=Example VerifyBamID Output= Verify BAM ID produces the following files: * *.genoCheck.depthRG * *.genoCheck.depthSM * *.genoCheck.selfRG * *.genoCheck.selfSM See [[VerifyBamID…'
=Example VerifyBamID Output=
Verify BAM ID produces the following files:
* *.genoCheck.depthRG
* *.genoCheck.depthSM
* *.genoCheck.selfRG
* *.genoCheck.selfSM
See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details.
== VerifyBamID Tutorial Output ==
The VerifyBamID output from the [[Tutorial: GotCloud| GotCloud Tutorial]] looks like this:
=== HG00096.genoCheck.depthRG ===
<pre>
#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
</pre>
=== HG00096.genoCheck.depthSM ===
<pre>
#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
</pre>
=== HG00096.genoCheck.selfRG ===
<pre>
#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
</pre>
=== HG00096.genoCheck.selfSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.depthRG ===
<pre>
#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</pre>
=== HG00100.genoCheck.depthSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.selfSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.selfRG ===
<pre>
#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
</pre>
Verify BAM ID produces the following files:
* *.genoCheck.depthRG
* *.genoCheck.depthSM
* *.genoCheck.selfRG
* *.genoCheck.selfSM
See [[VerifyBamID#Interpreting_output_files|VerifyBamID output documentation]] for more details.
== VerifyBamID Tutorial Output ==
The VerifyBamID output from the [[Tutorial: GotCloud| GotCloud Tutorial]] looks like this:
=== HG00096.genoCheck.depthRG ===
<pre>
#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
</pre>
=== HG00096.genoCheck.depthSM ===
<pre>
#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
</pre>
=== HG00096.genoCheck.selfRG ===
<pre>
#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
</pre>
=== HG00096.genoCheck.selfSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.depthRG ===
<pre>
#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</pre>
=== HG00100.genoCheck.depthSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.selfSM ===
<pre>
#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
</pre>
=== HG00100.genoCheck.selfRG ===
<pre>
#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
</pre>
