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  • blueskypy
    replied
    -stand_emit_conf 10.0 means that it won’t report any potential SNPs with a quality below 10.0; but unless they meet the quality threshold set by -stand_call_conf (50.0, in this case), they will be listed as failing the quality filter

    Leave a comment:


  • ymc
    replied
    Originally posted by biomichael View Post
    I got some information in the following site: http://www.broadinstitute.org/gsa/ga...tand_call_conf

    In the 1000 genomes project for pilot 2 (deep coverage of ~35x) we expect the raw Qscore > 50 variants to contain at least ~10% FP calls. We use extensive post-calling filters to eliminate most of these FPs. Variant Quality Score Recalibration is a tool to perform this filtering.

    -stand_call_conf [50.0]
    -stand_emit_conf 10.0

    So, I guess the -stand_emit_conf parameter is to lower the FPs(false positive?) got by the -stand_call_conf parameter. if -stand_call_conf=50 and -stand_emit_conf=10, the variants between 10 and 50 will be emitted but also marked as filtered.

    I don't know whether I understand rightly.
    Based on my experimentation, decreasing the -stand_emit_conf argument will simply increase number of LowQual calls but have virtually none effect on the PASS calls. So I don't think FP rate will change unless you also count LowQual calls as positives.

    Leave a comment:


  • biomichael
    replied
    I got some information in the following site: http://www.broadinstitute.org/gsa/ga...tand_call_conf

    In the 1000 genomes project for pilot 2 (deep coverage of ~35x) we expect the raw Qscore > 50 variants to contain at least ~10% FP calls. We use extensive post-calling filters to eliminate most of these FPs. Variant Quality Score Recalibration is a tool to perform this filtering.

    -stand_call_conf [50.0]
    -stand_emit_conf 10.0

    So, I guess the -stand_emit_conf parameter is to lower the FPs(false positive?) got by the -stand_call_conf parameter. if -stand_call_conf=50 and -stand_emit_conf=10, the variants between 10 and 50 will be emitted but also marked as filtered.

    I don't know whether I understand rightly.

    Leave a comment:


  • Rubal7
    replied
    No, not solved it yet

    Leave a comment:


  • jchoo
    replied
    not yet now, maybe the forum of Broad may help……

    Leave a comment:


  • biomichael
    replied
    Originally posted by Rubal7 View Post
    Hello all,

    I am using GATK unified genotyper to call snps from multiple low coverage samples. I have lowered the -stand_call_conf threshold to 4 as recommended under these circumstances. However should I also be lowering -stand_emit_conf to the same level? My uncertainty arises because I am not clear of the difference between calling snps and emitting snps. Could someone kindly clarify this for me or point me in the right direction?

    Many thanks,

    Rubal7
    I also encontered the same problem. Have you solved the problem?

    Leave a comment:


  • jchoo
    replied
    the same question, need help too~~

    Leave a comment:


  • Rubal7
    started a topic SNP calling vs emitting variants

    SNP calling vs emitting variants

    Hello all,

    I am using GATK unified genotyper to call snps from multiple low coverage samples. I have lowered the -stand_call_conf threshold to 4 as recommended under these circumstances. However should I also be lowering -stand_emit_conf to the same level? My uncertainty arises because I am not clear of the difference between calling snps and emitting snps. Could someone kindly clarify this for me or point me in the right direction?

    Many thanks,

    Rubal7

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