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
shows the results I would like to obtain.
Data 2 shows the results of Picard tools S
AM/BAM Alignment Summary Metrics 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 S
AM/BAM Alignment Summary Metrics 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