Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • #2
    the same question, need help too~~

    Comment


    • #3
      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?

      Comment


      • #4
        not yet now, maybe the forum of Broad may help……

        Comment


        • #5
          No, not solved it yet

          Comment


          • #6
            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.

            Comment


            • #7
              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.

              Comment


              • #8
                -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

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Strategies for Sequencing Challenging Samples
                  by seqadmin


                  Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                  03-22-2024, 06:39 AM
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 06:37 PM
                0 responses
                11 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, Yesterday, 06:07 PM
                0 responses
                10 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                51 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                67 views
                0 likes
                Last Post seqadmin  
                Working...
                X