SamSifter Help

Frequently Asked Questions

None so far...

Known Bugs

Please report new bugs to f.aldehoff@student.uni-tuebingen.de.

Bugs in SamSifter

  • The ‘Export to Bash’ dialog fails to save the file when SamSifter has been started from the GNOME/KDE/Unity menu. Saving SSX files works fine, however. Workaround: Save Workflow to SSX, close SamSifter, open SamSifter from Shell and retry exporting the Bash script.

Bugs in Tools used by SamSifter

  • BetterRMDup fails when processing MALT’ed files. This is actually a bug of the SAM parsing library used in BetterRMDup that does not handle the custom MALT @mm record properly. The bug has been reported and will be fixed in a future version.
  • SAMtools view reports a possibly truncated file and complains about a missing EOF marker. This is likely a bug in either MALT and/or SAMtools view which can be safely ignored. See http://sourceforge.net/p/samtools/mailman/samtools-help/thread/4EC52844.3090808@broadinstitute.org/ for details. It is caused by a missing compression flag when processing uncompressed files.
  • SAMtools view complains about inconsistency of the sequence length when compared to the CIGAR string. This is a bug in MALT 0.0.12 that has been reported. Please re-MALT your files with a newer version or remove the affected reads manually.

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