etc/salus/extract_bam_tag.sh

   1 #!/usr/bin/env bash
   2
   3 # https://gist.github.com/Shians/a95c49bda68481fb0adc83600d9eb6b8
   4 # called by
   5 # sh extract_bam_tag.sh input.bam BC
   6 # to print read_id and BC tag value
   7
   8 # two arguments, a bam file and the tag to extract
   9 BAM=$1
  10 TAG=$2
  11
  12 # write a tsv with columns read_id and tag value
  13 echo -e "read_id\t$TAG"
  14 samtools view "$BAM" | grep "$TAG:." | perl -pe 's/(^.+?)\t.*'$TAG':.:(.+?)\t.*/$1\t$2/g'
  15 # regular expression substutes pattern (read_id)*(tag_value)* for (read_id)\t(tag_value)