extract all the cigar sequences

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

cigar

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updated 8.6 years ago by cschu181 276 • | written 8.6 years ago by KVC_bioinfo 61

1 answer

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

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written 8.6 years ago by cschu181 276

works perfectly. Thank you so much

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written 8.6 years ago by KVC_bioinfo 61

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