Some more light on how to use the reference files.

[ankushreddy]

Hi Team,
Am actually using the TCGA data to run on the guacamole. I am confused like where should I pass the human reference hg19 file to variant calling or genotyping. Something like we use it in the avocado. Just want to check with you do we have to pass the reference file or is it going to take case of the reference file internally.

Could you please suggest me some good tools or is there any class in guacamole where we can sort the bam file and get the output as a bam file.

Thanks & Regards,
Ankush Reddy.

[ryan-williams]

Hi @ankushreddy! If you are calling variants on a BAM that is already MD-tagged, then you shouldn't need to pass in a reference.

Per @arahuja's work on #376, the --reference-fasta and --recompute-md-tags arguments to germline-threshold should allow you recompute MDTags on reads.

lmk if that doesn't make sense