samtools

samtools view -S HY_chr1_9653-9853.sort.v1.sam -b >H_chr1_9653-9853.sort.v1.bam

samtools index HBY_chr1_20307743-24307743.sort.v1.bam

samtools view -T ./homo_virus.fa  -h virus_HBY.txt>virus_HBY_0523.bam

samtools view -h -Sb virus_HBY_0523.sam >virus_HBY_0523.bam

samtools view HBY.sort.bam chr5:9653-9853 >HBY_chr5_9653-9853.sam

samtools index HBY_chr21_9653-9853.bam

samtools view -h HBY.bam chr1:1230-3230. | samtools view -Sb - >HBY_chr1_1230-3230.bam && samtools index HY_chr1_1230-3230.bam

samtools sort  HY.bam -o HY.sort.bam

samtools view -b HY.bam chr1 >HY_chr1.sort.bam

seqtk sample -s150 1.clean.fq.gz 100000 | seqtk seq -a - >Sample.10W.fa

samtools flagstat markdup.recal.bam

samtools view map.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > map.fa

samtools view -@ 36 -bF 4 -h sorted.markdup.recal.bam>sorted.mapping_h.bam

samtools view -@ 36 -bF 12 -h sorted.markdup.recal.bam>sorted.mapping_F12.bam