Hi GATK/Picard team,

I am trying to convert illumina infinium gtc files to vcf using 

java -jar picard.jar GtcToVcf \
      INPUT=input.gtc \
      REFERENCE_SEQUENCE=reference.fasta \
      OUTPUT=output.vcf \
      EXTENDED_ILLUMINA_MANIFEST=chip_name.extended.csv \
      CLUSTER_FILE=chip_name.egt \
      ILLUMINA_NORMALIZATION_MANIFEST=chip_name.bpm.csv \
      SAMPLE_ALIAS=my_sample_alias \

In order to generetate the `EXTENDED_ILLUMINA_MANIFEST` file after much searching I found this command 

java -jar $PICARD CreateExtendedIlluminaManifest \
INPUT=chip_name.bpm.csv \
OUTPUT=chip_name.extended.csv \
REPORT_FILE=??? \
CLUSTER_FILE=chip_name.egt \
REFERENCE_SEQUENCE=reference.fasta

By searching further, I came across two other community posts, only one of which is relevant and still seems unresolved: https://gatk.broadinstitute.org/hc/en-us/community/posts/4404560028571-How-do-I-run-CreateExtendedIlluminaManifest-myself-for-GtcToVcf-for-a-customized-Illumina-chip- 

Its still not clear what file should be used with the `REPORT_FILE` flag. Can this be downloaded somewhere? Do we need to generate this file ourselves? Checking the source code has also been futile: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/arrays/illumina/CreateExtendedIlluminaManifest.java

Would it be possbile to add documentation on how to properly generate vcf files from illumina binary .gtc files and which steps are needed. 

Best, 

James Gallant