Meaning of the column of sam file

Question

[Jimpix]

Hello! Referring to this columns in sam file:

1. QNAME
2. FLAG
3. RNAME
4. POS
5. MAPQ
6. CIGAR
7. RNEXT
8. PNEXT
9. TLEN
10. SEQ
11. QUAL

I wanted to ask how to extract the information about end position of the read? Morover if I want to know which strand it is, it will be depend on FLAG? If the FLAG is 16 that mean it is reverse and in the other cases it will be forward?

Answer 1

[Pierre Lindenbaum]

I wanted to ask how to extract the information about end position of the read?

you have to 'walk' over the CIGAR string. C Api For Bam: Iterating Over A Cigar String. https://stackoverflow.com/questions/39710796 , or you can use a tool like "bedtools bamtobed"

If the FLAG is 16 that mean it is reverse and in the other cases it will be forward?

if it's mapped, yes

[Jimpix]

Thanks for the answer! Why is not enought just to POS add length of SEQ?

[GenoMax]

Because alignment may contain soft-clipped sequence.

[Pierre Lindenbaum]

and indels...