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Primer clipping does not work correctly for small sequencing inserts

Status: Open.

#18 In tommyau/bamclipper;

· jaudetnml opened on Feb 17, 2026

Suggest adding parameter -o for output path

Status: Open.

#17 In tommyau/bamclipper;

· JuleBrenningmeyer opened on Sep 27, 2023

Negative strand genes

Status: Open.

#16 In tommyau/bamclipper;

· ceromova opened on May 10, 2023

clipping is not working if deletions follows the primer site

Status: Open.

#15 In tommyau/bamclipper;

· MarieLataretu opened on Apr 24, 2023

3' end clipping not working

Status: Open.

#14 In tommyau/bamclipper;

· donutbrew opened on Jul 7, 2020

Overlapping amplicons

Status: Open.

#13 In tommyau/bamclipper;

· aledj2 opened on May 10, 2020

Sam Flag

Status: Open.

#10 In tommyau/bamclipper;

· OldManTae opened on May 5, 2018

Picard Compatibility

Status: Open.

#9 In tommyau/bamclipper;

· OldManTae opened on Feb 23, 2018

Output metrics

Status: Open.

#8 In tommyau/bamclipper;

· OldManTae opened on Nov 29, 2017

ValidateSamFile detects errors in BAM files after soft-clipping primers with BamClipper

Status: Open.

#7 In tommyau/bamclipper;

· garrulus-glandarius opened on Oct 18, 2017

Marked and unmarked bases when clipping against the primer sequences

Status: Open.

#4 In tommyau/bamclipper;

· PromitaBose opened on Jun 5, 2017