Utilities/ReHeadSNtags.sh at master · EDitt/Utilities

33 lines (26 loc) · 1.11 KB

#PBS -S /bin/bash

#PBS -q batch

#PBS -N Change_SNtags_SAMheader

#PBS -l nodes=1:ppn=6

#PBS -l walltime=5:00:00

#PBS -l mem=10gb

#PBS -m abe

### This script changes the SN SAM tag header lines

### using a .txt file with the first column being the old SN name (and first part of filename)

### and the second column the new SN name

module load SAMtools/1.10-GCC-8.2.0-2.31.1

# 1st column old name, 2nd column, new name:

KEY="/scratch/eld72413/Salty_Nut/CultivatedOnly/Plate1_InbredKEY.txt"

# Input BAM files

RH_INPUT="/scratch/eld72413/Salty_Nut/CultivatedOnly/SNPcalling/Plate1_Bams"

# Output (reheadered) BAM files

RH_OUTPUT="/scratch/eld72413/Salty_Nut/CultivatedOnly/SNPcalling/Plate1_Bams/Test_Rehead"

while read line; do

SN1=$(echo "$line" | awk '{print $1}')

SN2=$(echo "$line" | awk '{print $2}')

file=$(find $RH_INPUT -maxdepth 1 -name "$SN1[!0-9]*.bam")

name=$(basename ${file%%.bam}"") #sample ID

echo "Changing sample name from $SN1 to $SN2 for sample $name"

samtools view -H ${file} | sed -e "s/SM:${SN1}/SM:${SN2}/g" | samtools reheader - $file > ${RH_OUTPUT}/${name}_reheadered.bam

done < $KEY

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