samtools extract sequence from bam file

Charles-Alexandre Roy answered on April 26, 2021 Popularity 1/10 Helpfulness 8/10

answer samtools extract sequence from bam file

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# 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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Tags: bam extract file samtools sequence shell

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Contributed on Apr 26 2021

Charles-Alexandre Roy

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