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Non-GVS bits required for GVS [VS-971] #8362

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merged 5 commits into from
Jun 27, 2023
Merged

Non-GVS bits required for GVS [VS-971] #8362

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1c25535
renamed VCF header
mcovarr Jun 8, 2023
1feea0f
Monitoring script support for VQSR Lite WDL JointVcfFiltering.wdl
mcovarr Jun 13, 2023
fdc09c7
run test with dummy monitoring script
mcovarr Jun 21, 2023
e7edf9e
Move rather than delete GVS BigQuery classes
mcovarr Jun 23, 2023
dc44285
Process Sample gVCF headers during Ingest [VS-836]
mcovarr Jun 23, 2023
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renamed VCF header
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@mcovarr
mcovarr committed Jun 26, 2023
commit 1c25535d850111ca76d2650a7e860d0a19944525
4 changes: 3 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFConstants.java
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Expand Up @@ -208,7 +208,9 @@ their names (or descriptions) depend on some threshold. Those filters are not i
public static final String VQSR_FAILURE_PREFIX = "low_VQSLOD_";
public static final String VQSR_FAILURE_SNP = VQSR_FAILURE_PREFIX + SNP;
public static final String VQSR_FAILURE_INDEL = VQSR_FAILURE_PREFIX + INDEL;
public static final String VQS_SENS_FAILURE_PREFIX = "low_VQS_SENS_";
// Prefix for a site (SNP/INDEL) that failed calibration sensitivity cutoff. In this case, the site would be a
// failure if the sensitivity is greater than the threshold.
public static final String VQS_SENS_FAILURE_PREFIX = "high_VQS_SENS_";
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Since this was confusing enough that it was gotten wrong initially maybe add a comment explaining what this means?

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It's analogous to the low_VQSLOD_ prefix - "Prefix for a site (SNP/INDEL) that failed calibration sensitivity cutoff". In this case, the site would be a failure if the sensitivity is greater than the threshold.

public static final String VQS_SENS_FAILURE_SNP = VQS_SENS_FAILURE_PREFIX + SNP;
public static final String VQS_SENS_FAILURE_INDEL = VQS_SENS_FAILURE_PREFIX + INDEL;

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