Spliced alignment information from bam file
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9.7 years ago
hadaarjan ▴ 20

How do I know if an alignment is spliced by looking at SAM format? I need to find spliced alignments from BAM file.

SAM BAM • 4.6k views
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2
Entering edit mode
9.7 years ago

search for 'N' in the cigar string?

samtools view  in.bam | awk '($6 ~ /N/)'
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