extract chimeric and multimap reads from bam file

Question

I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use htslib for parsing sam/bam files and extracting based on any flags. Any help on how to start will be appreciated.

Liam McIntyre · Answer

This is how I do it.
samtools view -@5 -f 0x800 -hb /path/sample.bam > sup.bam

Then if you want it as a fasta
samtools view -F 0x1 -hb sup.bam | samtools fasta -F 0x1 - > sup.fa

extract chimeric and multimap reads from bam file

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