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[CompareSAMs] comparison fails when comparing the same file

Status: Open.

#2053 In broadinstitute/picard;

· fgvieira opened on Jun 9, 2026

ValidateSamFile should accept secondary alignments without qualities

Status: Open.

#2050 In broadinstitute/picard;

· marcelm opened on Jun 4, 2026

Stable structured (JSON) ProgressLogger output mode for downstream parsers

Status: Open.

#2046 In broadinstitute/picard;

· carstenerickson opened on May 16, 2026

ProgressLogger could log rejected count alongside processed

Status: Open.

#2045 In broadinstitute/picard;

· carstenerickson opened on May 16, 2026

Documentation spelling mistake REMOVE_DUPLICATE -> REMOVE_DUPLICATES

Status: Open.

#2042 In broadinstitute/picard;

· mmterpstra opened on Mar 27, 2026

CollectHsMetrics incorrectly clips "overlapping" reads whose mates are on other chromosomes!

Status: Open.

#2039 In broadinstitute/picard;

· tfenne opened on Mar 11, 2026

New release for cram 3.1 support

Status: Open.

#2037 In broadinstitute/picard;

· FelixMoelder opened on Mar 5, 2026

SamToFastq fails when one (but not both) reads have vendor-fail flag set

Status: Open.

#2036 In broadinstitute/picard;

· yfarjoun opened on Feb 9, 2026

SamToFastq: OutOfMemoryError: Java heap space

Status: Open.

#2029 In broadinstitute/picard;

· Joyjoyjoyc opened on Nov 8, 2025

CRAM 3.1 support

Status: Open.

#2028 In broadinstitute/picard;

· dpmccabe opened on Oct 21, 2025

GtcToVcf 'EXTENDED_ILLUMINA_MANIFEST' documentation/information

Status: Open.

#2023 In broadinstitute/picard;

· kloot opened on Sep 4, 2025

Multiple Error (?) Messages when building with gradle

Status: Open.

#2015 In broadinstitute/picard;

· schlaepferp opened on Jun 3, 2025