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inbroadinstitute/picard (press backspace or delete to remove)Hi!
On the webpage https://broadinstitute.github.io/picard/picard-metric-definitions.html#HsMetrics ; the HsMetrics output
named PCT_USABLE_BASES_ON_BAIT is defined as The number of aligned, de-duped, ...
ioguztuncay
- 3
- Opened 10 days ago
- #1996
The title says it all. When running against a version of hg38 that has many lower-cased bases, I get an error rate of
~Q3 while the OVERLAPPING_ERROR accumulator gives a more reasonable Q27 for the same ...
yfarjoun
- Opened 10 days ago
- #1994
Issue
RnaSeqMetrics is supported by CollectMultipleMetrics, but one of the required options for this tool,
RIBOSOMAL_INTERVALS, is not accepted. It is therefore not possible to specify ribosomal intervals ...
question
Redmar-van-den-Berg
- 2
- Opened 12 days ago
- #1991
When sorting several pre-sorted BAM files (either by query or coordinate) with different headers, is it possible to
merge them with MergeSamFiles keeping the original sorting?
I am working with very large ...
fgvieira
- 2
- Opened 20 days ago
- #1990
Hello,
I am in the progress of upgrading the version of picard in Debian.
When packaging version 3.3.0 I met the following issue:
java.lang.AssertionError: expected [100000] but found [100000.0] at ...
pgrt
- 3
- Opened on Dec 26, 2024
- #1987
documentation request
Documentation request
Tool(s) involved
CollectInsertSizeMetrics
Description
With the follow command I get a plot with blue region(i.e. RF reads). picard CollectInsertSizeMetrics ...
LingjunM
- 6
- Opened on Nov 28, 2024
- #1983
bug report and feature request
Feature request
Tool(s) involved
Tool name(s), special parameters? GATK
Description
Specify whether you want a modification of an existing behavior or addition of a ...
desmodus1984
- 2
- Opened on Aug 30, 2024
- #1978
Documentation request
Tool involved : CollectHsMetrics AT_DROPOUT
Description AT_DROPOUT calculation is described as For each GC bin [0..50] we calculate a = % of target territory, and b
= % of aligned ...
jcharlton67
- 1
- Opened on Aug 5, 2024
- #1973
Bug Report
Affected tool(s)
TargetMetricsCollector, HsMetricCollector, WgsMetrics
Affected version(s)
Latest public release version [3.20] Latest development/master branch as of [7/30/24]
Description ...
Patrick-Schlaeger-Broad
- Opened on Jul 30, 2024
- #1971
This issue seems to be present in the latest version as well. I have a collection of WGS bam files (# 100) and fast
algorithm works gracefully for most of them whereas only a few of them fail with the ...
gokalpcelik
- 9
- Opened on Jul 8, 2024
- #1970
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