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A real deletion x a false extended deletion?

brdidobrdido Posts: 27Member

Hello again,

please, we need help understanding a deletion detected by HC.

Here is the VCF line and the activeRegions output (attached):

MT 9190 . CTGCACGACAACACAT C 1057.73 VQSRTrancheBOTH99.00to99.90 AC=1;AF=0.500;AN=2;BaseQRankSum=1.935;ClippingRankSum=-0.516;DP=301;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=45.84;MQ0=0;MQRankSum=1.456;NEGATIVE_TRAIN_SITE;QD=0.23;ReadPosRankSum=0.625;VQSLOD=-1.682e+00;culprit=MQ;set=variant23 GT:AD:GQ:PL 0/1:51,11:99:1095,0,1411

As we can see in the image several reads confirm a 2bp deletion at 9204. But HC called a 16bp deletion (that was later on filtered out of our pipeline because of VQSR not passing our filter) that is supported only by one read. Those "Insertions" marked at the end of the reads are "N"s from masked adaptors.

I'm glad that HC tried to identify a bigger deletion, but shouldn't it call the 2bp deletion as well?

Thanks in advance, Rodrigo.

deletionRLB-activeRegions.png
1948 x 1023 - 94K

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