How to discard alignments from SAM/BAM file that have mismatches

[mahmad37]

Hi,

I have sequenced the mRNA of a heterologous library expressed in human cells using nanopore. Then I mapped the reads from the fastq files to the reference database of the library using the minimap.

Then I filtered the SAM file to retain the primary reads with high mapping quality. After this, I visualised the BAM file in IGV:

As you can see there are some reads having mismatches to the reference database. I checked even the highest mapping quality reads are having mismatches. While I am guessing that these reads are mapping to more than one variant in the library dataset, I am looking for a command line that I could use to discard such alignments from SAM/BAM file. Unlike the BWA aligner, the minimap does not generate the MD (Mismatching positions/bases) & XM (Number of mismatches in the alignment) flags in the SAM file. It generates the NM:i flag that informs about the mismatches and INDELS together, so this is not really helpful as I am just looking to discard alignments with mismatches.

I would really appreciate the help to discard alignments with mismatches from SAM/BAM file (better if I can also give a mismatch threshold). Thanks alot.

[rob-p]

You can pass —-MD to minimap2 during alignment if you want it to generate those tags. See the man page for further details.

Best,
Rob

[lh3]

Thanks, Rob!