源碼閱讀網(wǎng)MongoDb 實(shí)踐篇
轉(zhuǎn)換成BAM文件，sort, mark duplicates
java -jar $picard SortSam \
? ?INPUT=aligned_sample1.sam \
? ?OUTPUT=sorted_sample1.bam \
? ?SORT_ORDER=coordinate
java -jar $picard MarkDuplicates \
? ?INPUT=sorted_sample1.bam \
? ?OUTPUT=dedup_sample1.bam \
? ?METRICS_FILE=metrics_sample1.txt
#just mark, not remove. most tools in GATK will ingore the marked reads；If desired, duplicates can be removed using the REMOVE_DUPLICATE and REMOVE_SEQUENCING_DUPLICATES options.
java -jar $picard BuildBamIndex \
標(biāo)簽：
