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Handle situation with few or zero reads in TCap #917
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test this please |
java -Xms~{java_memory_size}m -Xmx~{max_heap}m -jar /usr/picard/picard.jar CollectMultipleMetrics \ | ||
INPUT=~{input_bam} \ | ||
OUTPUT=~{output_bam_prefix} \ | ||
PROGRAM=CollectInsertSizeMetrics \ |
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These do not need to be specified explicitly, because by default CollectMultipleMetrics runs CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, and QualityScoreDistribution. Adding them explicitly (without also PROGRAM=null
to clear the defaults) has no effect
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👍 looks good, and tested this on both regular samples and a no-reads sample
* CheckFingerprint can allow LOD 0 | ||
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# 1.12.12 | ||
2023-03-30 (Date of Last Commit) |
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2023-03-30 (Date of Last Commit) | |
2023-01-13 (Date of Last Commit) |
@@ -1,6 +1,11 @@ | |||
# 1.12.12 | |||
# 1.12.13 |
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looks like things have gotten out of order, this section should look like:
# 1.12.13
2023-03-30 (Date of Last Commit)
* CheckFingerprint can allow LOD 0
# 1.12.12
2023-01-13 (Date of Last Commit)
* Updated remaining uses of GATK to version 4.3.0.0
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minor changelog comment, otherwise looks good, ty!
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test this please |
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Closes #913
Currently on personal picard and gatk dockers, will require those changes before merging this.Updated to official dockers.