ClipReads last bases

dansilber

Hello Everybody, I have a question regarding how to indicate last bases of every read... The walker ClipReads with the option -CT 'n1,n2' is able to clip reads from position n1 upto position n2, so -CT '1-8' clips the first 8 bases of every read. Is there a way to indicate this walker to clip the last bases of every read? something like 'end-10, end'....

Thanks Daniel

Geraldine_VdAuwera

Hi Daniel,

That's not currently possible, sorry.

Mark_DePristo

Adding this mode to the ClipReads code should be relatively straightforward. Have a look at the ClipReads code in the gatk and we'd be happy to incorporate a patch.

dansilber

Thanks Geraldine,

Do you know how to edit the cigar string while soft clipping? I mean how to produce the new cigar from the old one after sot clippiing.. That is the tricky part to achieve a succesfull clipping, Knowing that would be easy to program any kind of clipping. Thanks again. Saludos

Daneil

Geraldine_VdAuwera

@dansilber asked: how to produce the new cigar from the old one after soft clipping

Have a look at the source code :
https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java