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danielecook/realign_bam.sh

Created August 7, 2021 00:49
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Remapping an aligned bam
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realign_bam.sh
# Source: https://lh3.github.io/2021/07/06/remapping-an-aligned-bam
samtools collate -Oun128 in.bam | samtools fastq -OT RG,BC - \
| bwa mem -pt8 -CH <(samtools view -H in.bam|grep ^@RG) ref.fa - \
| samtools sort -@4 -m4g -o out.bam -
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