Parsing Read ID's out of a SAM file
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7.5 years ago
SaltedPork ▴ 170

I need to get a list of the read ID's from a SAM file. Is anyone aware of any shortcuts to do this before I embark on writing a parser in Perl?

SAM Perl Parsing • 2.8k views
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writing a parser should be the absolute last ditch effort. For any - any - format, there are at least 2-3 parsers out there already.

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7.5 years ago

samtools view foo.sam | cut -f 1 would be quick and easy. You could also use grep and cut.

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Followed by | sort | uniq if that is the ultimate aim.

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