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GATK HaplotypeCaller MIXED variants delins

Hello GATK team !

I am facing a problem that I am not exactly sure your caller can address and I would need your opinion on that.
I use GATK last version (3.4.46) haplotypeCaller to call my variants (after all the best practices).

I am getting the following two variants :
chr17 41222982 . ATTC A 8447.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;ClippingRankSum=-0.136;DP=515;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.02;MQRankSum=1.616;QD=16.40;ReadPosRankSum=-19.399;SOR=0.470 GT:AD:DP:GQ:PL 0/1:292,223:515:99:8485,0,17722
chr17 41222986 . T TAAAA 8363.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=-12.032;ClippingRankSum=0.954;DP=515;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.02;MQRankSum=-1.440;QD=16.24;ReadPosRankSum=-19.368;SOR=0.453 GT:AD:DP:GQ:PL 0/1:292,223:515:99:8401,0,17731

These is 1 deletion directly followed by 1 insertion. As you can see, the number of reads harbouring the reference (292) versus the alternate (223) is exactly the same. The problem is that my biologists are looking one single mutation called "delins" and because HC calls 2 distinct variants, I have 2 annotations and not 1 (should be something like c.1234delTTCinsAAAA).

Do you have any idea how I could handle that using HC ? Or maybe after getting the vcf with a post processing tool ?

Thanks a lot.


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by Sheila

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