extract all the cigar sequences

Question

[KVC_bioinfo]

hello all,

I want to extract all the cigar sequences from bam file and write them in a text file. Is anyone aware of any way to do this?

TIA

Answer 1

[cschu181]

samtools view your_bamfile.bam | cut -f 6 > your_textfile.txt

[KVC_bioinfo]

works perfectly. Thank you so much