##исходные файлы и результирующие файлы с unpaired удалены

mkdir bwa_mem

bwa mem -t 12 ../../bwa/chr8.fna  ../../dna_seq/out_paired_SRR10720419_1.fastq.gz  ../../dna_seq/out_paired_SRR10720419_2.fastq.gz  > map_chr8.sam 2> log_mem

ls -h -s map_chr8.sam

samtools sort -o map_chr8.bam map_chr8.sam 2> log_bam

samtools index -@ 12 map_chr8.bam 

samtools flagstat -@ 12 map_chr8.bam > flagstat

samtools faidx ../bwa/chr8.fna -o chr8.fai

samtools view -h map_chr8.bam NC_000008.11 > reads_chr8.sam

samtools view -b reads_chr8.sam > reads_chr8.bam

samtools flagstat reads_chr8.bam > chr8_flagstat

samtools view -f 0x2 -bS reads_chr8.bam > right_reads_chr8.bam

samtools flagstat right_reads_chr8.bam > right_flagstat

samtools index right_reads_chr8.bam

picard MarkDuplicates -M metrix.file.txt -I right_reads_chr8.bam -O marked.bam

samtools flagstat marked.bam > marked_flagstat

cp log_mem ~/public_html/term3/block3/pr12

cp log_bam ~/public_html/term3/block3/pr12

cp flagstat ~/public_html/term3/block3/pr12

cp chr8_flagstat ~/public_html/term3/block3/pr12

cp right_flagstat ~/public_html/term3/block3/pr12

cp marked_flagstat ~/public_html/term3/block3/pr12