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<code>--samples</code> option does not work as dropin replacement for <code>--population-file</code>

Status: Open.

#42 In cademirch/clam;

· percyfal opened on Feb 12, 2026

clam collect followed by clam loci does not take population labels into account

Status: Open.

#41 In cademirch/clam;

· percyfal opened on Feb 12, 2026

CLAM loci fails with "region reference sequence does not exist" when processing many gVCF files

Status: Open.

#40 In cademirch/clam;

· elizakirsch0 opened on Feb 10, 2026

<code>clam loci</code> fails on gVCF

Status: Open.

#27 In cademirch/clam;

· bernard-kim opened on Dec 22, 2025

Output sum/mean of coverages of samples

Status: Open.

#25 In cademirch/clam;

· percyfal opened on Nov 25, 2025