Question: VariantAnnotation as.vranges with asterisk in ALT field
0
gravatar for Jeremy Leipzig
3.4 years ago by
Jeremy Leipzig70 wrote:

GATK has recently started using asterisks in the ALT field for certain variants (i believe a SNP and deletion at one site)

chr22    47461908    .    TAA    *    859.92    PASS    AC=2;AF=0.333;AN=6;BaseQRankSum=-3.105;ClippingRankSum=0.773;DP=119;FS=12.256;MLEAC=2;MLEAF=0.333;MQ=70;MQRankSum=0.042;QD=8.77;ReadPosRankSum=0.126;SOR=2.17;OLD_MULTIALLELIC=chr22:47461908:TAA/TA/*    GT:AD:DP:GQ:PL    0/1:16,14:30:99:350,0,527    0/.:20,0:39:99:193,254,652    0/1:17,15:32:99:347,0,483

This is causing the VRanges validator to crash

> variants <- as(vcf, "VRanges")

Error in validObject(.Object) : 

  invalid class “VRanges” object: if 'alt' is 'NA', then 'altDepth' should be 'NA'

 

using VariantAnnotation_1.16.4    and  GATK 3.4-46-gbc02625

variantannotation gatk • 860 views
ADD COMMENTlink modified 3.4 years ago by Michael Lawrence11k • written 3.4 years ago by Jeremy Leipzig70
Answer: VariantAnnotation as.vranges with asterisk in ALT field
2
gravatar for Michael Lawrence
3.4 years ago by
United States
Michael Lawrence11k wrote:

I removed the assertion in devel, 1.17.22.

ADD COMMENTlink written 3.4 years ago by Michael Lawrence11k
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