depersonalizebam

#!/bin/bash
#
# Depersonalize a bamfile (Remove CIGAR, SEQ, QUAL and additional columns information)
#
# See Samtools Specification: samtools.sourceforge.net/SAMv1.pdf
#
# Usage: ./depersonalizebam input.bam ReadLengthINT > output.bam
#
# 2014-01-30 helmuth@molgen.mpg.de
BAM=$1
READLENGTH=${2:-50}

samtools view -h $BAM | \
  awk -v CIGAR=$READLENGTH 'BEGIN \
  {
    FS="\t"
    OFS="\t"
  }
  {
    if (/^@/)
    { # Print header lines without modification
      print;
    }
    else
    { 
      # Update PNEXT (sense strand) or POS (minus strand) from CIGAR
      POS=$4
      CIG=CIGAR"M"
      PNEXT=$8
      TLEN=$9
      if ($6 !~ /CIG/ && TLEN != 0 && PNEXT != POS) 
      { #check if TLEN information is given, then it is paired end
	if ( and($2, 0x10) != 16) 
	{ # sense strand
	  PNEXT=POS + TLEN - CIGAR
	}
        else
	  { # antisense strand (FAKE START introduction)
	  POS=PNEXT - TLEN - CIGAR
	}
      }

      if ($NF ~ /YT:Z/) 
      {
	# Put out bowtie alignment score
      	#         YT:Z:<S> Value of UU indicates the read was not part of a pair.
      	#         Value of CP indicates the read was part of a pair and the pair
      	#         aligned concordantly. Value of DP indicates the read was part
      	#         of a pair and the pair aligned discordantly. Value of UP
      	#         indicates the read was part of a pair but the pair failed to
      	#         aligned either concordantly or discordantly.
      	#         (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#sam-output)
      	# Output 11 columns: QNAME FLAG RNAME POS  MAPQ CIGAR RNEXT PNEXT TLEN  SEQ  QUAL YT/YZ
      	print                $1,   $2,  $3,   POS, $5,  CIG,  "=",  PNEXT,TLEN, "*", "*", $NF 
      }
      else
      {
	# Output 10 columns: QNAME FLAG RNAME POS  MAPQ CIGAR RNEXT PNEXT TLEN  SEQ  QUAL
	print                $1,   $2,  $3,   POS, $5,  CIG,  "=",  PNEXT,TLEN, "*", "*"
      }
    }
  }' | samtools view -bS -