What is difference between soft-clipped and hard-clipped in SAM specification?

Question

[mangfu100]

Hi.

I know that what soft-clipped reads are.

But when facing sam files, also, there are many hard clipped reads.

and I cannnot figure out what differences between them even though I check the sam specification.

Could you explain the difference of them?

I attached the easily understood figure

Answer 1

[Pierre Lindenbaum]

soft-clipped: bases in 5' and 3' of the read are NOT part of the alignment.

hard-clipped: bases in 5' and 3' of the read are NOT part of the alignment AND those bases have been removed from the read sequence in the BAM file. The 'real' sequence length would be length(SEQ)+ count-of-hard-clipped-bases

[Calvin]

May i ask that is there any particular reason to use soft-clipped and hard-clipped? Can i say in the case of soft-clipped, bases that are not part of the alignment can be aligned to its complementary sequence?

[Dataman]

@Calvin: This might answer your question: Difference between Hard Clip and Soft Clip in Samtools CIGAR string

Answer 2

[paulorapazote]

Hi Guys,

Full explanation about clipping: http://davetang.org/wiki/tiki-index.php?page=SAM