Tagged with #qualbydepth
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A new tool has been released!

Check out the documentation at QualByDepth.

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Hello,

I am hoping to perform hard filtering on some variants from a sequencing project where, unfortunately, I do not have information from enough samples for VQSR. I was planning to filter on the QD value, but it seems to be very low for variants that seem reasonable. Example:

chr7    55249063 .       G       A       225     PASS
AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=1.307;DP=4582;DP4=937,935,1299,1316;Dels=0.00;FQ=225;FS=0.323;
HaplotypeScore=390.2899;MQ=59.95;MQ0=0;MQRankSum=-1.910;PV4=0.81,1,1,1;QD=0.05;ReadPosRankSum=4.848;VDB=0.0003
GT:AD:GQ:PL     0/1:1917,2657:99:255,0,255

This variant is shown in IGV in the attached file- it looks to be a true positive, but because of the high depth, QD is very low. Based on the QD documentation, it looks as QD simply cannot be used to filter high-coverage data, since the value is QUAL/unfiltered depth.

Is there an alternative annotation that expresses the same measure, since QD is recommended in all the hard filtering documentation? Would GQ be a good substitute?

Your help is much appreciated!

Comments (14)

I had annotated raw indel file (given by UnifiedGenotyper), 1000G_omni2.5.b37.sites.vcf and hapmap_3.3.b37.sites.vcf with all possible annotations including QD (QualByDepth) using VariantAnnotator. However, i got an error when i tried to run VariantRecalibrator. It was complaing that QD has not been found in training variant. Is QD important annotation for indel filtering. Can it be ignored ?

P.S. - i did not use sample bam file while annotating training data set.

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INFO  15:11:55,999 RMDTrackBuilder - Loading Tribble index from disk for file NCBI_dbsnp_for_GATK.vcf
INFO  15:12:21,650 TraversalEngine -  chr1:128346793        1.98e+07   30.0 s        1.5 s      4.1%        12.1 m    11.6 m
INFO  15:12:51,650 TraversalEngine -  chr9:130658800        5.26e+07   60.0 s        1.1 s     53.9%       111.2 s    51.2 s
INFO  15:13:13,618 VariantDataManager - QD:      mean = NaN      standard deviation = NaN
INFO  15:13:16,417 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-13-g1706365):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Bad input: Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wiki/index.php/VariantAnnotator
##### ERROR ------------------------------------------------------------------------------------------