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Quickly remap BAM (from Heng Li post https://twitter.com/lh3lh3/status/1132756684789768202)
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| #!/bin/bash | |
| # | |
| # Quickly remap reads from BAM file to new reference | |
| # | |
| # Source: https://twitter.com/lh3lh3/status/1132756684789768202 | |
| # More details: https://janbio.home.blog/2019/05/30/useful-one-liners-collection/ | |
| # | |
| samtools collate -uOn128 old-pos-srt.bam tmpxyz \ | |
| | samtools fastq - \ | |
| | bwa mem -pt16 ref.fa - \ | |
| | samtools sort --threads=4 -m4G -o new-pos-srt.bam |
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