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More options for run_comethylation.sh #78

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PeteHaitch opened this issue Jun 12, 2014 · 1 comment
Closed

More options for run_comethylation.sh #78

PeteHaitch opened this issue Jun 12, 2014 · 1 comment

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@PeteHaitch
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In particular, the ability to pass TMP_DIR and VALIDATION_STRINGENCY to SortSam.
@PeteHaitch
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Update run_comethylation.sh to use samtools rather than Picard's SortSam; samtools sort -n does sort read_1 before read_2 provided it is v0.1.19 and not v0.1.18.

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@PeteHaitch