Split bwa mem for MergeBamAlignment

[dimo]

Hi team,

Struggling how to split bwa mem output into mapped vs unmapped to use with Picards MergeBamAlignment (to get MQ values).
Seems it doesn't like having the same read ids which means you have to be careful where one pair is unmapped while the other one is mapped.

Thanking you in advance.

[Biocomputronics]

The output is probably an alignment file in SAM/BAM format. Assuming that is the case, you can use 'SAMtools' to extract reads from an alignment file based on the bitwise flag in the SAM/BAM file.

Here is a link to SAMtools documentation:

http://www.htslib.org/doc/samtools.html

Here is a link to a tool that explains what flag value to use for each scenario.

https://broadinstitute.github.io/picard/explain-flags.html

for example you could do:

samtools view -f 4 alignment_file.bam

and it would return the alignment for unmapped reads.

samtools view -F 4 alignment_file.bam

would return all mapped reads.