Comments (4)
yfarjoun
commented on July 17, 2024
HsMetrics (and TargetedPcrMetrics) use a short array (as in short [] ) to calculate coverage metrics. This means that at each locus the coverage is limited by java MAX_SHORT which is ~32K...
There is currently no way to modify the behavior you are seeing.
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vdauwera
commented on July 17, 2024
We'll add this information to the docs if it's not already in there.
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dekling
commented on July 17, 2024
Incorporated explanation in to docs.
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dekling
commented on July 17, 2024
Incorporated explanation in to docs.
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Related Issues (20)
- MarkDuplicates: Instead of adding the read group of a read to the key, picard always adds "RG"
- java.lang.NegativeArraySizeException HOT 2
- genotypeConcordance irregular behavior in counting after applying filters HOT 3
- MarkDuplicates with single end data does not write the full report HOT 3
- Picard Build Failure HOT 6
- java environment not detected when using option OUTPUT in BuilBamIndex HOT 1
- Getting Segfault when running ReorderSam via GATK HOT 1
- How to control the number of threads HOT 1
- Edge case in LiftoverVcf causes cryptic string exception HOT 8
- TAGGING_POLICY=OpticalOnly tags everything HOT 4
- Issue Running Picard MarkDuplicates: File Compression Error with Snappy HOT 1
- about MarkDuplicates HOT 1
- UnMarkDuplicate HOT 1
- Running picard in parallel issue HOT 3
- `--USE_END_IN_UNPAIRED_READS` and `--USE_UNPAIRED_CLIPPED_END` options for `picard MarkDuplicates` have no effect HOT 9
- MarkDuplicates SAM validation error HOT 6
- Optical duplicates HOT 4
- ValidateSamFile wrong NM tag computation HOT 3
- CollectWgsMetrics error, out of bound of the index? HOT 8
- Lost output/information during RenameSampleInVcf HOT 11
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