Match reads from sam (first col) to fastq file and extract to a file
From sam file, I want to fetch the reads (first col. of sam file) of specific position (pos. column of sam file). After that, those reads are to be matched with FASTQ file and fetch those reads (4 lines, including qual. scores) to a new file.
Do we have any tool for it, or need to depend upon writing program? Can anyone suggest the procedure pls.
thanks,
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sofie_carolina •
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Thanks for the response. Can we do it using, faidx/tabix/picard ? I have gone through picard, I guess it allows the above requirement. If you are aware about it, pls share.