Galaxy Users, I would like to filter a .bam file to remove reads with low mapping quality, especially ambiguously mapped reads (MAPQ = 0). I can easily do this using the command line version of samtools as shown below. samtools view -bq 20 hba1.bam > hba1_MAPQ20.bam None of the options available under "NGS:SAM Tools" (e.g., Generate pileup and Filter SAM) provide an option for removing reads with low mapping quality. The history shown in http://main.g2.bx.psu.edu/u/onsongo/h/obtaininghighqualityreads shows the results I would like to obtain. Data 2 shows the results of Picard tools SAM/BAM Alignment Summary Metrics<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics> on hba1.bam which contains reads with MAPQ values less than 20. As shown in this summary html, PF_READS_ALIGNED = 775 and PF_HQ_ALIGNED_READS = 241. Data 4 shows the results of Picard tools SAM/BAM Alignment Summary Metrics<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics> on hba1_MAPQ20.bam which contains only reads with MAPQ greater than or equal to 20. As shown in this summary html, PF_READS_ALIGNED = 241 and PF_HQ_ALIGNED_READS = 241. Is there a way in Galaxy to filter a bam file to remove low quality mapped reads similar to using the samtools command line alternative shown above? Thanks, Getiria -- Getiria Onsongo, Ph.D. Bioinformatics Research Scientist Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455 Phone: 612-625-0101