4. Alignment sorting - SAMtools

#!/bin/bash
#PBS -l nodes=1:ppn=10
#PBS -l walltime=4:00:00

module load SAMtools/1.11-GCC-10.2.0

inds="1_10 1_8 \
2_11 2_1 2_3 2_5 2_7 2_9 \
3_11 3_1 3_3 3_5 3_7 3_9 \
4_11 4_2 4_3 4_4 4_8 \
5_2 5_4 \
6_10 6_12 6_1 6_6 6_7 \
7_10 7_11 7_12 7_1 7_3 7_4 7_6 7_7 7_8 7_9 \
8_10 8_11 8_12 8_2 8_5 8_6 8_7 8_8 8_9"

for ind in $inds; do

samtools view -Sb /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/mapped/$ind.mapped.sam > /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.output.bam

wait

samtools view -b -F 4 /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.output.bam > /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.mapped.bam

wait

samtools sort /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.mapped.bam > /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.sorted.bam

wait
    
samtools index /user/gent/427/vsc42733/BumbleBeeData/RawRADSeqData/sorted/$ind.sorted.bam

done