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Code Block
languagebash
samtools view yeast_pe.sort.bam | cut -f 6 | head -20

Next, make sure we're only looking at alignment records that represent mapped reads. The -F 0x4 option says to filter records where the 0x4 flag (read unmapped) is 0, resulting it only mapped reads being output.

Code Block
languagebash
samtools view -F 0x4 yeast_pe.sort.bam | cut -f 6 | head -20

Now we use grep with the pattern '[ID]' to select lines (which are now just CIGAR strings) that have Insert or Deletion operators. The brackets ( [ ] ) denote a character class pattern, which matches any of the characters inside the brackets. Be sure to ask for Perl regular expressions (-P) to be sure that this character class syntax is recognized.

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