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yvan edited this page Mar 18, 2015 · 1 revision

Excap 34

Sample mapping group NSC delivered mapping started mapping finished variant started variant finished SNP-ID delivered
14001029800-EEogPU NA 08/12/14 14:00:0 09/12/14 16:12:00 10/12/14 21:54:17 11/12/14 09:33:29 12/12/14 02:53:16 rs1137288 rs1446464 rs1057908 mismatched Rerun OK 12/12/14 11:25:00
14001020601-EEogPU NA 08/12/14 14:00:0 09/12/14 16:13:34 10/12/14 21:02:44 11/12/14 09:35:21 12/12/14 03:23:47 rs1137288 rs1446464 rs1057908 mismatched Rerun OK 12/12/14 11:25:00
14000998001-EEogPU NA 08/12/14 14:00:0 10/12/14 16:48:28 12/12/14 08:07:18 12/12/14 08:07:18 13/12/14 03:42:21 OK 16/12/14 11:30:00
14000997800-HSP NA 08/12/14 14:00:0 11/12/14 09:31:23 13/12/14 01:30:29 13/12/14 11:45:08 14/12/14 10:08:20 OK 16/12/14 11:30:00
14000987001-EEogPU NA 08/12/14 14:00:0 11/12/14 09:32:14 12/12/14 18:02:51 13/12/14 11:45:48 14/12/14 09:04:08 OK 16/12/14 11:30:00
14000981501-EEogPU 1 08/12/14 14:00:0 12/12/14 08:28:17 13/12/14 23:50:54 13/12/14 23:50:54 15/12/14 16:41:27 OK 16/12/14 11:30:00
14000977401-EEogPU 1 08/12/14 14:00:0 13/12/14 23:50:54 15/12/14 16:03:21 15/12/14 16:03:22 16/12/14 15:55:13 OK 17/12/14 08:30:00
14000977001-EEogPU 1 08/12/14 14:00:0 15/12/14 16:03:21 17/12/14 06:17:58 17/12/14 08:19:10 18/12/14 09:48:54 OK 05/01/15 13:15:00
14000970301-Bindevev 2 08/12/14 14:00:0 12/12/14 15:31:24 14/12/14 08:25:32 14/12/14 13:29:43 15/12/14 16:29:17 OK 16/12/14 11:30:00
14000942501-Bindevev 2 08/12/14 14:00:0 14/12/14 08:25:33 16/12/14 08:33:03 16/12/14 10:02:11 17/12/14 12:58:28 rs3736782 mismatched 17/12/14 13:15:00
14000657001-EEogPU 2 08/12/14 14:00:0 16/12/14 08:33:03 18/12/14 05:00:41 05/01/15 10:01:46 06/01/15 02:00:55 OK 06/01/15 11:35:00
14000390201-EEogPU 3 08/12/14 14:00:0 12/12/14 20:44:19 14/12/14 08:29:02 14/12/14 08:44:54 15/12/14 16:15:30 OK 16/12/14 11:30:00
14000067301-Bindevev 3 08/12/14 14:00:0 14/12/14 08:29:02 16/12/14 02:13:33 16/12/14 10:05:07 17/12/14 14:16:26 OK 17/12/14 14:20:00
14000032001-EEogPU 3 08/12/14 14:00:0 16/12/14 02:13:34 17/12/14 17:59:50 05/01/15 10:00:45 06/01/15 01:27:39 OK 06/01/15 11:35:00

PostProcess

12/12/2014

12/12/14 11:24:10 mv Sample_Diag-excap34-14001020601-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/
12/12/14 11:24:53 mv Sample_Diag-excap34-14001029800-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/

14/12/14 14:21:51 mv Sample_Diag-excap34-14000987001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/
14/12/14 14:22:06 mv Sample_Diag-excap34-14000998001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/
14/12/14 14:22:18 mv Sample_Diag-excap34-14000997800-HSP-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../HSP/

06/01/15 11:37:04 mv Sample_Diag-excap34-14000657001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/ 06/01/15 11:37:13 mv Sample_Diag-excap34-14000032001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX ../../EEogPU/

QC

Sample Q20 Q30 % Targets >= 10x % Targets >= 20x Mean Target Coverage Total Number of Variants Ti/Tv ratio number of nonsense variants skewed allele frequency:
XXXXXXXXXXX >80.0 >0.9 PASS >0.8 PASS >75 PASS 35000,55000 PASS 2,3 PASS < 100 PASS <0.05 PASS
14000987001 93.97 89.31 0.994774 0.987306 150.287447 52115 2.53300608103 72 0.0056
14001020601 93.52 88.53 0.996476 0.990115 166.607729 45553 2.54021830394 86 0.0047
14001029800 93.65 88.75 0.995324 0.988748 161.083112 45231 2.56262763784 65 0.0051
14000998001 93.97 89.28 0.995709 0.987991 157.349932 45025 2.58072558459 59 0.0048
14000997800 94.12 89.54 0.996203 0.988976 157.891605 45521 2.54717616362 82 0.0054
14000942501 94.10 89.51 0.995948 0.990772 190.747348 45190 2.55071847632004 62 0.0058
14000970301 92.98 87.61 0.99481 0.987113 158.077191 47480 2.55808305674735 99 0.0038
14000977001 94.04 89.36 0.996297 0.989813 172.057696 45155 2.55785440613027 67 0.0054
14000977401 94.06 89.38 0.996452 0.990167 174.991861 47430 2.54112239961297 81 0.0081
14000981501 94.18 89.61 0.995447 0.989371 169.446728 46012 2.55549979088248 75 0.0102
14000390201 92.88 87.48 0.995754 0.987992 156.61842 45412 2.54123798279642 72 0.006
14000657001 93.35 88.30 0.994693 0.987351 165.111645 45941 2.55866577271203 77 0.0063
14000067301 93.15 87.90 0.99684 0.991387 195.489991 45457 2.53895994614608 62 0.0048
14000032001 92.86 87.45 0.995748 0.987415 155.63985 48926 2.56644622894032 85 0.0056 
yvans@loki:/data/diag/diagInternal/samples/EEogPU/Sample_Diag-excap34-14000987001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX
> perl ../../141125_D00132.B.Project_Diag-excap34-2014-11-24/qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.994774 (>0.9) PASS
% Targets >= 20x : 0.987306 (>0.8) PASS
Mean Target Coverage : 150.287447 (>75) PASS

Variant Quality:
Total Number of Variants : 52115 (35000,55000) PASS
Ti/Tv ratio : 2.53300608103158 (2,3) PASS
Total number of nonsense variants: 72 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0056 (<0.05) PASS

yvans@loki:/data/diag/diagInternal/samples/EEogPU/Sample_Diag-excap34-14001020601-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX
> perl ../../141125_D00132.B.Project_Diag-excap34-2014-11-24/qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.996476 (>0.9) PASS
% Targets >= 20x : 0.990115 (>0.8) PASS
Mean Target Coverage : 166.607729 (>75) PASS

Variant Quality:
Total Number of Variants : 45553 (35000,55000) PASS
Ti/Tv ratio : 2.54021830394626 (2,3) PASS
Total number of nonsense variants: 86 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0047 (<0.05) PASS

yvans@loki:/data/diag/diagInternal/samples/EEogPU/Sample_Diag-excap34-14001029800-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX
> perl ../../141125_D00132.B.Project_Diag-excap34-2014-11-24/qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.995324 (>0.9) PASS
% Targets >= 20x : 0.988748 (>0.8) PASS
Mean Target Coverage : 161.083112 (>75) PASS

Variant Quality:
Total Number of Variants : 45231 (35000,55000) PASS
Ti/Tv ratio : 2.56262763784888 (2,3) PASS
Total number of nonsense variants: 65 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0051 (<0.05) PASS

yvans@loki:/data/diag/diagInternal/samples/EEogPU/Sample_Diag-excap34-14000998001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX
> perl ../../141125_D00132.B.Project_Diag-excap34-2014-11-24/qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.995709 (>0.9) PASS
% Targets >= 20x : 0.987991 (>0.8) PASS
Mean Target Coverage : 157.349932 (>75) PASS

Variant Quality:
Total Number of Variants : 45025 (35000,55000) PASS
Ti/Tv ratio : 2.58072558459422 (2,3) PASS
Total number of nonsense variants: 59 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0048 (<0.05) PASS

yvans@loki:/data/diag/diagInternal/samples/HSP/Sample_Diag-excap34-14000997800-HSP-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX
> perl ../../141125_D00132.B.Project_Diag-excap34-2014-11-24/qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.996203 (>0.9) PASS
% Targets >= 20x : 0.988976 (>0.8) PASS
Mean Target Coverage : 157.891605 (>75) PASS

Variant Quality:
Total Number of Variants : 45521 (35000,55000) PASS
Ti/Tv ratio : 2.54717616362259 (2,3) PASS
Total number of nonsense variants: 82 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0054 (<0.05) PASS

16/12/14

yvans@loki:/data/diag/diagInternal/samples/141125_D00132.B.Project_Diag-excap34-2014-11-24/Sample_Diag-excap34-14000970301-Bindevev-v01-KIT-Av5
> perl ../qualityControl.pl
Coverage Quality:
% Targets >= 10x : 0.99481 (>0.9) PASS
% Targets >= 20x : 0.987113 (>0.8) PASS
Mean Target Coverage : 158.077191 (>75) PASS

Variant Quality:
Total Number of Variants : 47480 (35000,55000) PASS
Ti/Tv ratio : 2.55808305674735 (2,3) PASS
Total number of nonsense variants: 99 (< 100) PASS
The ratio of SNPs with skewed allele frequency: 0.0038 (<0.05) PASS

17/12/2014

<pre. yvans@loki:/data/diag/diagInternal/samples/141125_D00132.B.Project_Diag-excap34-2014-11-24/Sample_Diag-excap34-14000942501-Bindevev-v01-KIT-Av5

perl ../qualityControl.pl Coverage Quality: % Targets >= 10x : 0.995948 (>0.9) PASS % Targets >= 20x : 0.990772 (>0.8) PASS Mean Target Coverage : 190.747348 (>75) PASS

Variant Quality: Total Number of Variants : 45190 (35000,55000) PASS Ti/Tv ratio : 2.55071847632004 (2,3) PASS Total number of nonsense variants: 62 (< 100) PASS The ratio of SNPs with skewed allele frequency: 0.0058 (<0.05) PASS

yvans@loki:/data/diag/diagInternal/samples/141125_D00132.B.Project_Diag-excap34-2014-11-24/Sample_Diag-excap34-14000067301-Bindevev-v01-KIT-Av5

perl ../qualityControl.pl Coverage Quality: % Targets >= 10x : 0.99684 (>0.9) PASS % Targets >= 20x : 0.991387 (>0.8) PASS Mean Target Coverage : 195.489991 (>75) PASS

Variant Quality: Total Number of Variants : 45457 (35000,55000) PASS Ti/Tv ratio : 2.53895994614608 (2,3) PASS Total number of nonsense variants: 62 (< 100) PASS The ratio of SNPs with skewed allele frequency: 0.0048 (<0.05) PASS

Fixing SNP fingerprinting error

16/12/14 09:51:56 34 16/12/14 10:01:33 tail -f yvan3samples2mapping.log yvan3samples3mapping.log
16/12/14 10:25:32 cd ../EEogPU/Sample_Diag-excap34-14001029800-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX/
16/12/14 10:27:06 cp 070_QC/snp.raw.snpFingerPrintingTest.report 060_delivery/Sample_Diag-excap34-14001029800-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX.snp.raw.snpFingerPrintingTest.report
16/12/14 10:28:10 cp 070_QC/snp.raw.snpFingerPrintingTest.report 060_delivery/Sample_Diag-excap34-14001020601-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX.snp.raw.snpFingerPrintingTest.report
16/12/14 10:28:28 cd ../Sample_Diag-excap34-14000998001-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX/
16/12/14 10:28:31 python /data/diag/diagInternal/diagnosticBundle/script/amg/fingerprinting/MergeResults.py
16/12/14 10:29:12 cd ../Sample_Diag-excap34-14001020601-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX/
16/12/14 10:29:36 chmod -r 770 ./
16/12/14 10:30:17 cd ../Sample_Diag-excap34-14001029800-EEogPU-v01-KIT-Av5.141125_D00132_0090_BC5MWFANXX/
16/12/14 10:30:22 chmod -R 770 ./
16/12/14 10:30:25 chgrp -R ous-diag ./

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