Tag_CB_UMI.sh

#!/bin/bash

# Peter van Galen, 191004
# Move cell barcode (CB) and unique molecular identifier (UMI) from read identifier to sam tags.
# Resulting bam file will have tags for cell barcode (CB) and UMI (UB) as per 10X convention, https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-bam
# These tags are required to run maegatk software

# Example execution:
# Tag_CB_UMI.PvG191004.sh <bam>

use -q Samtools

# First variable is bam file to convert
INPUT=$1
# Second variable is bam file to write (automatically named)
OUTPUT="$(echo "${INPUT/bam/10x.bam}")"

echo "Converting $INPUT into $OUTPUT..."

samtools view -h $INPUT | awk 'BEGIN{FS="\t"; OFS="\t"} {
	if (substr($1,1,1) == "@") {
		print $0
	} else {
		split($1, a, "_")
		$1=""
		print a[1]"_"a[2]$0"\tCB:Z:"a[3]"-1\tUB:Z:"a[4]
	} }' | samtools view -bh > $OUTPUT

echo "Done!"

date

exit 0