Closed dbrami closed 6 years ago
In this log entry, it's specifically referring to the manifest file that was used when the GTC file was created, not the manifest file that was provided on the command-line for gtc_to_vcf.py.
I see - maybe worth clarifying slightly then
Even when the following command is used:
gtc_to_vcf.py \ --gtc-paths \ $GTDIR/idats_with_GTCs/202238520009/ \ --manifest-file \ $GTDIR/GSA-24v1-0_C1.csv \ --genome-fasta-file \ ~/ReferenceData/grch37/grch37.fa \ --output-vcf-path \ $GTDIR/vcf \ --log-file \ $GTDIR/vcf/gtc_to_vcf.log 1> $GTDIR/gtc2vcf.out 2> $GTDIR/gtc2vcf.err &
the following is found in the logs:
2018-07-14 17:19:05,734 - GTC converter - INFO - Manifest file used for GTC conversion identified as: GSA-24v1-0_C1.bpm
The .BPM file does indeed exist in the same folder as .CSV but I did not use the "skip-indels" flag