Question: How I know a file is sam or bam, sorted or unsorted
12 months ago by
Arup Ghosh ♦ 2.7k
Check the bam/sam file header line using samtools
samtools view -H Aligned.out.sam |grep "@HD" if you see
SO:coordinate is present, it means the output is sorted. For STAR sorted/unsorted output check the STAR aligner manual section 4.3 .
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