Dear Biostar community,
I have a bwa mapping of metagenomic sequencing reads on assembled contigs. I also have a list of IDs of "interesting" contigs. Now I would like to subset the mapping (bam/sam file) to obtain a mapping (bam/sam file) that only contains my desired contigs. Do you know of any simpel way (samtools, picard tools, R, Scala/Java) to do so? Note please that creating a mapping with a reduced contig.fasta file is not an option for me.
Thank you in advance!