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Show an example of complete workflow with MPI tools #48

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fredjarlier opened this issue Oct 29, 2020 · 1 comment
Open

Show an example of complete workflow with MPI tools #48

fredjarlier opened this issue Oct 29, 2020 · 1 comment
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documentation Improvements or additions to documentation

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@fredjarlier
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The idea is to build a complete pipeline from fatsq to markduplicate using MPI tools and samtools
mpiBWA + samtools fixmate + mpiSORT + samtools markduplicate (+ samtools merge).
@fredjarlier fredjarlier added the documentation Improvements or additions to documentation label Oct 29, 2020
@fredjarlier
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Pipeline tested in dev

mpiBWAByChr ( -f ) + mpiSort ( -b -u chrID ) + samtools index -@ 8 + samtools markdup -@ 8

sounds good so far...

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@fredjarlier