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Old 08-24-2016, 01:55 AM   #1
dovah
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Default sam format: SEQ field

Hi

I have a question regarding SAM format. What does it represent the field $10 (SEQ)? Checking SAM format manual (https://samtools.github.io/hts-specs/SAMv1.pdf), if I get it right, SEQ is the sequence of the aligned portion of the read, counting alignment matches and insertions from CIGAR field ($6). So if I count the number of characters in this field ($10), I can get the length of the mapped fragment of the read, isn't it? If I wanted to calculate the reference length at the mapping site, I should in this case sum the alignment matches and deletions from CIGAR field ($6), right? So what does the TLEN field ($9) represents?

Thanks in advance
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Old 08-24-2016, 01:40 PM   #2
Brian Bushnell
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tlen is for paired reads; it indicates the total length of the original fragment, if the reads map in a properly paired configuration. To calculate the length of an alignment, you need to add all the symbols except for insertions (I) and potentially clipping (S/H).
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