GenotypeGVCFs can't handle somatic GVCFs from DRAGEN 3.8.4

[ldgauthier]

Bug Report

Affected tool(s) or class(es)

GenotypeGVCFs

Affected version(s)

• [x] Latest public release version [version?]
• [x] Latest master branch as of [date of test?]

Description

GenotypeGVCFs won't joint call DRAGEN mitochondrial data because of the DRAGEN somatic output format.

We should be able to use the DRAGEN SQ in place of Mutect2's TLOD (see line 279 in GenotypeGVCFsEngine) Note that DRAGEN SQ is a Phred-scaled double

Steps to reproduce

DRAGEN somatic GVCF entries from version 3.8.4 look like: chrM 1 . G <NON_REF> . weak_evidence END=1 GT:AD:DP:SQ:MIN_DP 0/0:112,1579:1691:0:1691

Run GenotypeGVCFs with -V to a file like that (reference GenotypeGVCFsIntegrationTest::testGenotypingForSomaticGVCFs() for more details) Must include --input-is-somatic as of now

Expected behavior

The task should run to completion, calculating a site quality store using the DRAGEN SQ value

Actual behavior

Error from AlleleFrequencyCalculator about not having PLs or GQ.

[ldgauthier]

Replaces #7797