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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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logs usage of BPM file when CSV is invoked #16

Closed dbrami closed 6 years ago

dbrami commented 6 years ago

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

KelleyRyanM commented 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.

dbrami commented 6 years ago

I see - maybe worth clarifying slightly then