filter gtc using probe file

[cmccabe0728]

Is it possible in BeadArrayFiles to filter a gtc file using a probe id file, that would return a new gtc with only the probe_id in the text file? I have tried

from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest 

but that doesn't seem to support writting back directly to the gtc. So I tried sub-process to create an filtered gtc using the metadata from the original gtc, but that doesn't appear to be working. Thank you.

probe_id.txt
exm518984 
ilmnseq_rs1800462_ilmnfwd_F2BT_deg3a1b1_ilmndup2_IlmnRep
ilmnseq_rs1800462

[jzieve]

The short answer is no, at least not easily. To actually filter the GTC, you would need to alter the manifest and the norm transform lookups. I would not recommend that approach. I would recommend further downstream filtering of the GTC itself so while converting to gtc_final_report, VCF, (or whatever downstream file format), doing the filtering then.