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
shows the results I would like to obtain.
Data 2 shows the results of Picard tools SAM/BAM Alignment Summary
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
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?
Getiria Onsongo, Ph.D.
Bioinformatics Research Scientist
Masonic Cancer Center,
University of Minnesota
Minneapolis, MN 55455
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