genome-sampler mask¶
Apply pre-computed alignment mask to filter positions.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
- mask:
AlignmentMask Definition of positions to be masked based on one or more sequences in the alignment.[required]
Parameters¶
- level:
Str%Choices('mask', 'caution') The level that masking should be performed at. "mask" will mask only positions annotated as "mask", while "caution" will mask positions annotated as "mask" or "caution".[default:
'mask']- mask_terminal_gaps:
Bool Mask alignment positions that are terminal (i.e., end) gaps in all reference sequences.[default:
True]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The alignment with masked positions removed.[required]
- Bolyen, E., Dillon, M. R., Bokulich, N. A., Ladner, J. T., Larsen, B. B., Hepp, C. M., Lemmer, D., Sahl, J. W., Sanchez, A., Holdgraf, C., Sewell, C., Choudhury, A. G., Stachurski, J., McKay, M., Engelthaler, D. M., Worobey, M., Keim, P., & Gregory Caporaso, J. (2020). Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. F1000 Research, 9(657), 657. 10.12688/f1000research.24751.1