Skip to content

issues Search Results · repo:broadinstitute/picard language:Java

Filter by

812 results
 (96 ms)

812 results

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
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Restrict your search to the title by using the in:title qualifier.
Issue origami icon

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues
ProTip! 
Restrict your search to the title by using the in:title qualifier.
Issue search results · GitHub