/Shell/Bash/Samtools extract sequence from bam file

Samtools extract sequence from bam file

Samtools extract sequence from bam file

# Basic syntax:
# For a BAM file:
samtools view file.bam | cut -f 10 > output.txt

# For a SAM file:
cut -f 10 file.sam > output.txt

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Source: seqanswers.com

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