Hi Getiria,

Galaxy does not have a tool to do this directly (but it would be a nice addition). Converting to SAM and using a combinations of tools in Text Manipulation would likely be possible. It would involve several steps and some experimentation, but a workflow could be created from that result to do the filter at all once in the future.


Sorry that we could not help more,

Best,

Jen
Galaxy team

On 10/24/11 9:15 AM, Getiria Onsongo wrote:
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 <tel:612-625-0101>




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