GTC files cannot be listed through both command interface and file list when only submitting a .txt file

[freeseek]

GTC files cannot be listed through both command interface and file list when only submitting a .txt file

[freeseek]

The problem is that your csv_manifest_file and your egt_cluster_file variables contain spaces, so they are interepreted as additional options, i.e., additional GTC files that are not allowed when using the --gtcs command. Simply use quotes as follows to make it work:

bcftools +gtc2vcf
--no-version
--bpm $bpm_manifest_file
--csv "$csv_manifest_file"
--egt "$egt_cluster_file"
--gtcs ./gtc_list_file.txt
--fasta-ref $ref
--output $out_prefix.vcf
--output-type v
--extra $out_prefix.tsv
--verbose

Notice that using the option -Ou and the option --output-type v, while allowed, is incorrect as the later option will simply override the former option. Also, do notice that the csv_manifest_file can be input as a gzipped file

[hsmith9002]

Thank you for the quick response!. That seemed to fix that, but now I' getting this: "Header of file ./ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv is incorrect:".

The csv is attached.
GTC_GDA_test_0826_ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv

Thank you
Harry

[freeseek]

Ah yeah, the manifest file name did seem weird to me. That's because GTC_GDA_test_0826_ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv is more like a file report. You need to use the .csv manifest file for the GDA array that you can find here

[hsmith9002]

I think I got it working using the _A2.csv.gz. I'm using the _A2.bpm.