How to convert extended CIGAR to regular CIGAR

Question

[artemd]

So I have a sam file with extended CIGAR format like this:

17H87=1D12=1D2=3D32=1D4=2D5=2D13=....

And I want to convert it to a sam file containing regular CIGAR format that will look like this:

17S83M1D14M1D4M3D31M1D2M2D6M...

(they do not represent the same reads... I want only to visualize the problem)

Anyone knows some software/script that will convert sam/bam with extended CIGAR to a sam/bam with regular CIGAR? It seems like a standard problem that might already have a solution so I want to ask here before solving it the hard way(coding)

[cschu181]

Assuming you have a .sam named old.sam

 samtools view -Sh old.sam |  awk '/^@/ {print $0; next;} {$6=gensub(/[=X]/, "M", "g", $6); print $0;}' > new.sam

Disclaimer: I haven't tested this on a real samfile, as I don't have one available right now

Argh. No. Wrong. Sorry. Disregard the first version.

Edits: Misread what you wanted at first, now it should replace = and X in extended with M.

[artemd]

Thanks for the reply, looks very elegant and probably will work for times when rapid testing is needed.

Answer 1

[GenoMax]

reformat.sh from BBMap suite can do this: reformat.sh in=orig.sam out=new.sam sam=1.3

[artemd]

Forgot to say thanks, so thanks. Will be using this (I used BBmap for trimming/filtering, strangely in their manual for reformat there is no mention of CIGAR at all) manual

[GenoMax]

Developers probably get to the manual updates last. I think @Brian pretty much single-handedly develops BBMap suite so we should cut him a bit of slack :)

[artemd]

Sure, I'm not complaining or berating. Just was stating that although I used the tool I didn't know I could use it for this purpose as well. Great tool overall. Thanks for your help.

Answer 2

[Pierre Lindenbaum]

I've quickly written one: https://github.com/lindenb/jvarkit/wiki/Biostar234081

 $ cat toy.sam 
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  1M2X5=4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG*XX:B:S,12561,2,20,112

 $ java -jar dist/biostar234081.jar toy.sam 
@HD VN:1.5  SO:unsorted
@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG*XX:B:S,12561,2,20,112

[artemd]

Thanks, I checked the code and it seems like it would handle this problem in a robust fashion. I expected something exactly like this to exist somewhere, and now that you have built it (very fast) it exists here.

Thanks again.