参考

简书 | 从BAM文件提取unmapped reads并转换成fastq格式

PCR 去重

java -jar /opt/biosoft/picard-tools/picard.jar MarkDuplicates \
I=A1.test.bam \
O=A1.test.markdup.bam \
CREATE_INDEX=true \
REMOVE_DUPLICATES=true \
M=A1.marked_dup_metrics.txt

bam2fasta

paired or unpaired