Closed hsmith9002 closed 2 years ago
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 $out_prefix.tsv
--verbose
Notice that using the option -Ou
and the option --output-type v
, while allowed, is incorrect as the later option will simply override the former option. Also, do notice that the csv_manifest_file
can be input as a gzipped file
Thank you for the quick response!. That seemed to fix that, but now I' getting this: "Header of file ./ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv is incorrect:".
The csv is attached. GTC_GDA_test_0826_ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv
Thank you Harry
Ah yeah, the manifest file name did seem weird to me. That's because GTC_GDA_test_0826_ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv
is more like a file report. You need to use the .csv
manifest file for the GDA array that you can find here
I think I got it working using the _A2.csv.gz. I'm using the _A2.bpm.
Hi,
I am getting the error message "GTC files cannot be listed through both command interface and file list" even though I am only submitting a single .txt file with a list of the gtc file names. I have tried this where the actual gtc files are in the directory where I am running the script, and also where they are in their own directory. I am running on a google cloud instance and using a singularity container. Here is the code, and I have attached the gtc_list file.
`bpm_manifest_file="./GDA_PGx-8v1-0_20042614_A2.bpm" csv_manifest_file="./ProjectDetailReport ILMN GDA 07-11-22 AMS1.csv" egt_cluster_file="./GDA FINAL 3 plate validation reclustered 06302022.egt" path_to_gtc_folder="./gtc_file_list.csv" ref="./GRCh38_full_analysis_set_plus_decoy_hla.fa" # or ref="$HOME/GRCh37/human_g1k_v37.fasta" out_prefix="206486390022"
singularity exec gtc2vcf_072922.sif bcftools +gtc2vcf \ --no-version -Ou \ --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 `
Thank you Harry gtc_list_file.txt