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Alignment workflow for PCR-free #384

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PedalheadPHX opened this issue Oct 1, 2020 · 1 comment
Closed

Alignment workflow for PCR-free #384

PedalheadPHX opened this issue Oct 1, 2020 · 1 comment

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@PedalheadPHX
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  • Markdups should then only occur at lane level, but then stats need to be merged
@PedalheadPHX
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@bryce-turner Plan is to test the new BWA-MEM2 release:
Chunk lane FASTQ
align lane chunks with BWA-MEM2, pipe to ST-fixmate, pipe to ST-sort.
ST-Merge lane chunks
ST-Markdups
ST-Merge lane level post markdup BAM if data on multiple lanes
If multiple lanes the Markdup stats will need to be summarized to get final stats

Will need to determine if pipling this new version of bwa to samtools causes the performance boost to be lost

@bryce-turner bryce-turner mentioned this issue Jul 8, 2021
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@PedalheadPHX @bryce-turner