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# VariantAnnotator not annotating genotype columns

Member Posts: 19

Hi,

Could you tell me how to encourage GATK to annotate my genotype columns (i.e. add annotations to the FORMAT and PANC_R columns in the following file):

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PANC_R
chrX 259221 . GA G 136.74 . AC=2;AF=1.00;AN=2;DP=15;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=8.82;MQ0=1;QD=3.04 GT:AD:GQ:PL 1/1:0,2:6:164,6,0


The file was generated with HaplotypeCaller. I used a command line similar to this one to no effect:

java -jar \$GATKROOT/GenomeAnalysisTK.jarT VariantAnnotator -R hg19_random.fa -I chr7_recalibrated.bam -V chr7.vcf --dbsnpdbSNP135_chr.vcf -A Coverage -A QualByDepth -A FisherStrand -A MappingQualityRankSumTest -A ReadPosRankSumTest -o chr7_annotated-again.vcf
`

Does anyone have any suggestions? Thanks in advance!

Tagged:

• Member, Dev Posts: 543 ✭✭✭✭

All of the annotations you specified in your call to HC are INFO-level annotations, and I think are in your vcf (the RankSum annotations only apply to het variants, so I wouldn't expect to see them in your example line). To my knowledge, there are no extra FORMAT (or sample) level annotations available

• Member Posts: 19

The background to this comment is that I'm trying to run VariantRecalibration on these data and I need the FORMAT column to have the DP annotation in order to follow Best Practices. http://gatkforums.broadinstitute.org/discussion/comment/7761/#Comment_7761

I have definitely seen other examples on this site where GATK-generated VCF files have DP annotation in the FORMAT column. http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk Is it because I'm using HaplotypeCaller instead of UnifiedGenotyper? What can I do to encourage these annotations to appear?

• Member, Dev Posts: 543 ✭✭✭✭

VariantRecalibration also works on the INFO-level DP field, which is present.

I haven't tracked the recent changes to HC too closely, it's possible that FORMAT-DP was removed, and it's possible that it was only removed for indels. I'm not sure

• Member Posts: 19

When I run VariantRecalibrator for SNPs on this VCF, I get the error message " Bad input: Values for DP annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. ". Every variant does have DP in the INFO column, but not in the FORMAT column.

• Member Posts: 19
edited July 2013

Oh, I see... I got so excited about having a potential answer that I ran with it! Thanks for the answers @pdexheimer

Geraldine Van der Auwera, PhD

• Member, Dev Posts: 543 ✭✭✭✭

Hmm, I thought I'd seen that error recently, and in searching a little bit I found that @Geraldine_VdAuwera and I are giving you exactly opposite advice. I think I'm right, but you never know...

I do see that someone previously tracked this type of error to a malformed VCF: http://gatkforums.broadinstitute.org/discussion/2254/variantrecalibrator-reports-not-finding-annotations-that-are-present