Changes between Version 1 and Version 2 of BIOS_SampleBlacklist2


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Timestamp:
Sep 19, 2016 5:04:41 PM (13 months ago)
Author:
jamverlouw
Comment:

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  • BIOS_SampleBlacklist2

    v1 v2  
    55
    66== QC flag ==
    7 These three samples are flagged because of too low number of reads:[[BR]] Too few reads:[[BR]] AC1JV9ACXX-1-10[[BR]] AD1NE2ACXX-5-22[[BR]] BD1NW4ACXX-3-27[[BR]] [[BR]] Other reasons: See http://www.bbmriwiki.nl/wiki/FgQualityControl/FgQualityControlRun1 [[BR]] BD1NYRACXX-6-10 too low percentage of mapped reads, outlier on principal component 1,4,5,6[[BR]] AD2CJPACXX-8-9 low exon correlation, outlier on principal component 1,11,14[[BR]] BD1NR9ACXX-7-27 low percentage of mapped reads, outlier on principal component 4, likely degraded[[BR]]
     7These three samples are flagged because of too low number of reads:[[BR]] Too few reads:[[BR]] AC1JV9ACXX-1-10[[BR]] AD1NE2ACXX-5-22[[BR]] BD1NW4ACXX-3-27[[BR]] [[BR]] Other reasons: See http://www.bbmriwiki.nl/wiki/BIOS_QualityControl/BIOS_QualityControlRun1 [[BR]] BD1NYRACXX-6-10 too low percentage of mapped reads, outlier on principal component 1,4,5,6[[BR]] AD2CJPACXX-8-9 low exon correlation, outlier on principal component 1,11,14[[BR]] BD1NR9ACXX-7-27 low percentage of mapped reads, outlier on principal component 4, likely degraded[[BR]]
    88
    99== Genotype concordance ==
    10 This is the list of the samples from the different cohorts that have a mismatch between RNA and DNA genotypes that could not be corrected since there is no additional lab evidence suggesting a sample swap. For more information, see http://www.bbmriwiki.nl/wiki/FgSampleBlacklist [[BR]] '''CODAM:'''[[BR]] AD10W1ACXX-5-18[[BR]] AD10W1ACXX-8-11[[BR]] '''LL:'''[[BR]] AC1C40ACXX-4-4[[BR]] AD1GWFACXX-4-15 [[BR]] '''RS:'''[[BR]] AD1NNNACXX-4-18[[BR]] AC1JV9ACXX-1-13[[BR]] BC1JTJACXX-6-7[[BR]] BC1KAVACXX-8-13[[BR]] '''LLS:'''[[BR]] BD1NW4ACXX-7-13[[BR]]BD1NYRACXX-2-27[[BR]]BC1KBKACXX-5-8[[BR]]AD1NAMACXX-7-19[[BR]]BC1KBKACXX-5-6[[BR]]AD2DATACXX-8-1[[BR]]BD2D5MACXX-4-15[[BR]]BD2D5MACXX-3-7[[BR]]AD2DATACXX-3-21[[BR]]AD2DATACXX-4-5[[BR]]AD1NFNACXX-8-25[[BR]]BD24PGACXX-7-8[[BR]]BD2CPRACXX-1-12[[BR]]AD2DATACXX-3-22[[BR]]BD24PGACXX-7-10[[BR]]BD2CPRACXX-1-21[[BR]]BC1KBKACXX-5-3[[BR]]AD1NFNACXX-8-27[[BR]]BD24PGACXX-8-25[[BR]]BC1KBKACXX-5-7[[BR]]BD24PGACXX-6-12[[BR]]BD1NW4ACXX-8-5[[BR]]BC1KBKACXX-3-12[[BR]]BC1KBKACXX-5-1[[BR]]AD2CJPACXX-6-9[[BR]]BD1NYRACXX-2-16[[BR]]AD2CJPACXX-5-1[[BR]]AD1NE2ACXX-4-22[[BR]]BC1KBKACXX-5-2[[BR]]BC1KBKACXX-5-5[[BR]]BD1NYRACXX-3-1[[BR]]BD2D5MACXX-2-25[[BR]]BD1NYRACXX-4-19[[BR]]AD1NFNACXX-4-8[[BR]]BD1NYRACXX-2-15[[BR]]BC1KBKACXX-5-4[[BR]]AD1NFNACXX-5-15[[BR]]
     10This is the list of the samples from the different cohorts that have a mismatch between RNA and DNA genotypes that could not be corrected since there is no additional lab evidence suggesting a sample swap. For more information, see http://www.bbmriwiki.nl/wiki/BIOS_SampleBlacklist [[BR]] '''CODAM:'''[[BR]] AD10W1ACXX-5-18[[BR]] AD10W1ACXX-8-11[[BR]] '''LL:'''[[BR]] AC1C40ACXX-4-4[[BR]] AD1GWFACXX-4-15 [[BR]] '''RS:'''[[BR]] AD1NNNACXX-4-18[[BR]] AC1JV9ACXX-1-13[[BR]] BC1JTJACXX-6-7[[BR]] BC1KAVACXX-8-13[[BR]] '''LLS:'''[[BR]] BD1NW4ACXX-7-13[[BR]]BD1NYRACXX-2-27[[BR]]BC1KBKACXX-5-8[[BR]]AD1NAMACXX-7-19[[BR]]BC1KBKACXX-5-6[[BR]]AD2DATACXX-8-1[[BR]]BD2D5MACXX-4-15[[BR]]BD2D5MACXX-3-7[[BR]]AD2DATACXX-3-21[[BR]]AD2DATACXX-4-5[[BR]]AD1NFNACXX-8-25[[BR]]BD24PGACXX-7-8[[BR]]BD2CPRACXX-1-12[[BR]]AD2DATACXX-3-22[[BR]]BD24PGACXX-7-10[[BR]]BD2CPRACXX-1-21[[BR]]BC1KBKACXX-5-3[[BR]]AD1NFNACXX-8-27[[BR]]BD24PGACXX-8-25[[BR]]BC1KBKACXX-5-7[[BR]]BD24PGACXX-6-12[[BR]]BD1NW4ACXX-8-5[[BR]]BC1KBKACXX-3-12[[BR]]BC1KBKACXX-5-1[[BR]]AD2CJPACXX-6-9[[BR]]BD1NYRACXX-2-16[[BR]]AD2CJPACXX-5-1[[BR]]AD1NE2ACXX-4-22[[BR]]BC1KBKACXX-5-2[[BR]]BC1KBKACXX-5-5[[BR]]BD1NYRACXX-3-1[[BR]]BD2D5MACXX-2-25[[BR]]BD1NYRACXX-4-19[[BR]]AD1NFNACXX-4-8[[BR]]BD1NYRACXX-2-15[[BR]]BC1KBKACXX-5-4[[BR]]AD1NFNACXX-5-15[[BR]]
    1111
    1212== Contaminations ==