gravatar for madiha_shabbir46

2 hours ago by

Hi,

I am extracting some regions(in txt file) from bam file using following command

      cat ref.txt | xargs samtools view -b in.bam -o out.bam

But it doesn't return whole list of reference instead miss few from the end.
My question is:

  1. is there any limit on extracting references from bam file?
  2. is there any other way to do the same job

Replies on few posts suggested to use region in bed format, I couldn't figure out how to convert .txt file into .bed file.

Any lead would be appreciated 🙂

TIA



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