#Commands used for mtDNA filtering:
#map reads
bwa index *.fasta
bwa mem -t 60 *.fasta *_1.fq | samtools sort -@ 10 -l 9 -O BAM -o for_sort.bam
bwa mem -t 60 *.fasta *_2.fq | samtools sort -@ 10 -l 9 -O BAM -o rev_sort.bam

#create ids files
perl bam2fqs.pl for_sort.bam 2> ids_for
perl bam2fqs.pl rev_sort.bam 2> ids_rev

#filter ids
grep -P "No_hit" ids_for | cut -f1 > ids_for_no_mt
grep -P "No_hit" ids_rev | cut -f1 > ids_rev_no_mt

#create list for paired reads
cat ids_for_no_mt ids_rev_no_mt | sort | uniq -c | awk '$1==2{print $2}' > paired.ids_no_mt

#extract reads from genome
seqtk subseq *_1_val_1.fq paired.ids_no_mt > *_1.confilter.fq
seqtk subseq *_2_val_2.fq paired.ids_no_mt > *_2.confilter.fq
