GenomeSTRiP SVGenotyper not producing genotypes

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Laura Cottino

• September 25, 2020 11:48

Hi, 

We ran SVGenotyper on our VCF output from the CNVDiscovery pipeline, however, the GT and GQ fields in the resulting VCF are empty (they just have a ".") for all of the CNVs. This is an example for one of the CNVs:

"""

1 9124572 CNV_1_9124572_9125672 G <CNV> . PASS END=9125672;GCFRACTION=0.47;GCLENGTH=1101;GLALTFREQ=NA;GLALTSUM=0.000;GLHETSUM=0.000;GLINBREEDINGCOEFF=NA;GLREFFREQ=NA;GLREFSUM=0.000;GSCALLRATE=1.000;GSCLUSTERSEP=6.59;GSCLUSTERSEPWEIGHTEDMEAN=5.73;GSCLUSTERSEPWEIGHTEDMEDIAN=5.62;GSCNALLELES=2;GSCNCATEGORY=DEL;GSCNDIST=0,1,453;GSCNMAX=2;GSCNMIN=1;GSCNQUAL=0.4832;GSDUPLICATEOVERLAP=NA;GSDUPLICATES=NA;GSDUPLICATESCORE=NA;GSELENGTH=1101;GSEXPMEAN=71.3606;GSGMMWEIGHTS=0.0082,0.0082,0.9836,0.0000;GSM1=1.0230;GSM2=0.2432,1.2162;GSNNONREF=1;GSNONVARSCORE=NA;GSNVARIANT=1;GSVDJFRACTION=0.000;SVTYPE=CNV GT:CN:CNF:CNL:CNP:CNQ:FT:GQ:GSPC .:2:2.2118:-1000.00,-20.51,-0.00,-2.73:-1000.00,-22.59,0.00,-25.15:99.0:PASS:.:0 .:2:1.8976:-250.71,-11.02,-0.00,-5.67:-252.79,-13.10,-0.00,-28.09:99.0:PASS:.:0 .:2:1.9830:-271.14,-13.20,-0.00,-4.85:-273.22,-15.28,-0.00,-27.27:99.0:PASS:.:0 .:2:1.5809:-150.03,-2.88,-0.00,-7.17:-152.11,-4.96,-0.00,-29.59:49.6:PASS:.:0 .:2:1.8424:-224.80,-9.11,-0.00,-5.86:-226.88,-11.19,-0.00,-28.28:99.0:PASS:.:0 .:2:1.9328:-250.11,-11.49,-0.00,-5.15:-252.19,-13.57,-0.00,-27.58:99.0:PASS:.:0 .:2:2.1839:-316.39,-18.26,-0.00,-2.82:-318.47,-20.34,0.00,-25.24:99.0:PASS:.:0 .:2:1.8725:-237.09,-10.06,-0.00,-5.72:-239.17,-12.14,-0.00,-28.15:99.0:PASS:.:0 .:2:1.9649:-261.49,-12.48,-0.00,-4.93:-263.56,-14.56,-0.00,-27.35:99.0:PASS:.:0 .:2:2.2497:-319.62,-19.24,-0.00,-2.07:-321.40,-21.31,0.00,-24.49:99.0:PASS:.:0 .:2:2.1272:-304.39,-16.87,-0.00,-3.40:-306.47,-18.95,0.00,-25.83:99.0:PASS:.:0 .:2:2.1276:-283.08,-15.68,-0.00,-3.17:-285.16,-17.76,0.00,-25.59:99.0:PASS:.:0

"""

Do you know why this is happening/have a solution for this?

Thank you,

Laura

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• 

  Genevieve Brandt (she/her)

  • September 25, 2020 18:24

  Bob Handsaker

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  Bob Handsaker

  • September 28, 2020 12:01

  The diploid genotypes for CNVs are encoded in the CN / CNQ fields, analogous to GT and GQ. CN is the diploid copy number estimate and CNQ is the quality. There is also CNF which is a fractional "point estimate" of the copy number from read depth alone. And CNL gives the likelihood of each copy number class (starting from zero).

   

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