Tagged with #baseqranksum
0 documentation articles | 0 announcements | 5 forum discussions

No articles to display.

No articles to display.

Created 2015-11-10 15:38:11 | Updated | Tags: clippingranksumtest variantfiltration baseqranksum

Comments (1)

Hi team,

I was hoping to filtered out variants with extreme rank sum values for base qual and clipping, with: echo "date +%y/%m/%d_%H:%M:%S.... Mark bad quality variants .... " GenomeAnalysisTK -R local_reference/dm6.fa \ -T VariantFiltration \ -V ${input_vcf} \ -filter "MQ<60" -filterName "lowMQ" \ -filter "BaseQRankSum<-4" -filterName "lowBQSR" \ -filter "BaseQRankSum>4" -filterName "highBQSR" \ -filter "ClippingRankSum<-2.5" -filterName "lowCRS" \ -filter "ClippingRankSum>2.5" -filterName "hiCRS" \ -filter "QD<5.0" -filterName "LowQD" \ -filter "FS>30" -filterName "hiSB" \ -G_filter "DP<10" -G_filterName "lowIDP" \ -o ${input_vcf}_marked.vcf

but it returns : WARN 15:12:34,785 Interpreter - ![0,12]: 'BaseQRankSum > 4;' undefined variable BaseQRankSum WARN 15:12:34,786 Interpreter - ![0,12]: 'BaseQRankSum < -4;' undefined variable BaseQRankSum WARN 15:12:34,786 Interpreter - ![0,15]: 'ClippingRankSum < -2.5;' undefined variable ClippingRankSum WARN 15:12:34,787 Interpreter - ![0,15]: 'ClippingRankSum > 2.5;' undefined variable ClippingRankSum

I thought this information could be filtered on. What am I doing wrong ?



Created 2015-09-09 21:56:12 | Updated 2015-09-09 21:56:49 | Tags: inbreedingcoeff variantannotator mqranksum baseqranksum

Comments (7)

Hi @Team,

I found that VariantAnnotator sometimes does not annotate some annotations that are requested.

A ) The Rank Sum Test annotations MQRankSum & BaseQRankSum I was not able to identify the requirements that have to be met, so they are being calculated for a variant.

B ) InbreedingCoeff This one seems to be connected to the number of total called alleles (AN). For me there needed to be at least 10% alleles be called (19/186). The doc for that says [1] "at least 10 founder samples". Maybe this has to be updated to 10%?

These are the ones I observed. Can someone tell me more about that?

Thanks, Alexander

[1] https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_InbreedingCoeff.php

Created 2015-07-29 01:58:31 | Updated | Tags: filtering baseqranksum

Comments (3)


I was plotting the distribution of BaseQRankSum and noticed a large number of variants with a BaseQRankSum outside of Z-score of +/- 2, which suggests that a lot of variants have significant base quality differences between the REF and ALT. I plotted the distribution of ClippingRankSum, MQRankSum, and ReadPosRankSum and the majority of variants had Z-scores inside +/- 2.

Is this typical and what is this suggestive of? I followed the best practices for DNA sequencing using GATK3.

I found this post (http://gatkforums.broadinstitute.org/discussion/2035/z-scores-for-baseqranksum), which is similar to what I'm asking but has a different distribution of Z-scores.

Thank you in advance.


Created 2014-04-23 14:29:03 | Updated | Tags: baseqranksum

Comments (1)

Hi, Why does BaseQRankSum annotation tag appear just in some variants? Which is the differences between variants with this tag and those without it? Thanks

Created 2013-05-09 16:40:31 | Updated | Tags: unifiedgenotyper mqranksum readposranksum baseqranksum glm

Comments (2)

I have run UnifiedGenotyper with the -glm options SNP and BOTH. These two approaches yield identical variants and identical genotype likelihoods (at least the first 100k variants I checked). However, a few of the annotations have different values: BaseQRankSum MQRankSum ReadPosRankSum

-glm SNP on the left and -glm BOTH on the right:

MQRankSum=-1.762 MQRankSum=-1.785

MQRankSum=-5.307 MQRankSum=-4.970

MQRankSum=0.262 MQRankSum=-0.022

MQRankSum=-0.680 MQRankSum=-0.710

MQRankSum=1.016 MQRankSum=0.231

MQRankSum=-0.693 MQRankSum=-0.681

MQRankSum=-0.839 MQRankSum=-0.830

MQRankSum=1.924 MQRankSum=1.889

MQRankSum=-0.991 MQRankSum=-0.665

MQRankSum=-0.459 MQRankSum=-0.958

BaseQRankSum=-1.803 BaseQRankSum=-1.881

BaseQRankSum=6.918 BaseQRankSum=6.894

BaseQRankSum=-2.512 BaseQRankSum=-2.524

BaseQRankSum=2.000 BaseQRankSum=2.020

BaseQRankSum=2.095 BaseQRankSum=2.006

BaseQRankSum=2.134 BaseQRankSum=2.223

BaseQRankSum=-3.622 BaseQRankSum=-3.547

BaseQRankSum=1.569 BaseQRankSum=1.586

BaseQRankSum=-3.416 BaseQRankSum=-3.733

BaseQRankSum=-1.745 BaseQRankSum=-1.769

ReadPosRankSum=-0.341 ReadPosRankSum=-0.280

ReadPosRankSum=4.207 ReadPosRankSum=4.190

ReadPosRankSum=-3.809 ReadPosRankSum=-3.832

ReadPosRankSum=-2.047 ReadPosRankSum=-2.060

ReadPosRankSum=-1.279 ReadPosRankSum=-1.232

ReadPosRankSum=-3.921 ReadPosRankSum=-3.955

ReadPosRankSum=-1.500 ReadPosRankSum=-1.486

ReadPosRankSum=-0.374 ReadPosRankSum=-0.403

ReadPosRankSum=3.209 ReadPosRankSum=3.188

ReadPosRankSum=1.889 ReadPosRankSum=1.868

Why is that?

I noticed another user got different variants, but I get the same variants and the same likelihoods: [http://gatkforums.broadinstitute.org/discussion/1782/unifiedgenotyper-different-glm-value-result-in-different-sets-of-variants]

I ran single threaded.

I use MQRankSum and ReadPosRankSum for VariantRecalibrator, so it affects my downstream results, if the annotations are -glm dependent. Hence I am asking my question. I hope you can illuminate me. Thank you.