Clipping both ends with ClipReads

Follow

Chen Leibson

• May 08, 2024 11:56

GATK version used: 4.2.6.1
Exact command used: gatk ClipReads -I in.bam -O out.bam -CR HARDCLIP_BASES -CT "1-5"

Hi,

I'd appreciate any advice regarding clipping both ends of reads in BAM file with ClipReads. 

Running gatk ClipReads -I in.bam -O out.bam -CR HARDCLIP_BASES -CT "1-5" clipped the first 5 bases, but I couldn't figure out how to clip the last 5 bases as well. Setting -CT "1-5, -5--1", for example, resulted in an error:

java.lang.RuntimeException: Badly formatted cyclesToClip argument.

My reads have different lengths, so the number of cycles that are 5 from the end is different for each read. 

Thanks!

0

• 

  Gökalp Çelik

  • May 08, 2024 12:29

  Hi Chen Leibson

  GATK ClipReads does not have that functionality to clip reads dynamically from the ends but needs precise cycle numbers to clip, therefore our suggestion would be to use a different tool. Although we cannot provide direct support for it fgbio's ClipBam tool seems to do the job just as you expect.

  https://fulcrumgenomics.github.io/fgbio/tools/latest/ClipBam.html

  I hope this helps. 

   

  0

  Comment actions Permalink
• 

  Chen Leibson

  • May 08, 2024 12:36

  Okay, I'll try it out

  Thank you!

  0

  Comment actions Permalink

Please sign in to leave a comment.