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Asa Thibodeau authored and ajt986 committed Jul 12, 2021
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Expand Up @@ -73,12 73,16 @@ BAM Input Only:

`--bcidx` The column index (counting from 0) of the CSV file barcode to cell id map for the barcode. (Default: 0)

`--cellidx` The column index (counting from 0) of the CSV file barcode to cell id map for the cell id. (Default: 8)
`--cellidx` The column index (counting from 0) of the CSV file barcode to cell id map for the cell id. (Default: 0)

`--iscellidx` The column index (counting from 0) of the CSV file barcode to cell id map for determining if the barcode corresponds to a cell. (Default: 9)

`--mapqthresh` Threshold for filtering low map quality reads (<= comparison). (Default: 30)

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`--maxinsertsize` The maximum insert size (in bp) between read pairs. (Default: 900)
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Examples:

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