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Old 02-02-2012, 07:39 AM   #1
Rubal7
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Default 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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Old 03-28-2012, 07:29 PM   #2
jchoo
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the same question, need help too~~
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Old 05-11-2012, 12:48 AM   #3
biomichael
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Quote:
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?
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Old 05-11-2012, 12:51 AM   #4
jchoo
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not yet now, maybe the forum of Broad may help……
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Old 05-11-2012, 12:56 AM   #5
Rubal7
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No, not solved it yet
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Old 05-11-2012, 01:11 AM   #6
biomichael
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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.
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Old 05-11-2012, 02:31 AM   #7
ymc
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Quote:
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.
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Old 05-13-2013, 11:15 AM   #8
blueskypy
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-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
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