Question: Removing Low Quality Reads
0
Getiria Onsongo • 40 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
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modified 7.1 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.1 years ago by
Getiria Onsongo • 40
