Open ytao0210 opened 1 year ago
@ytao0210 Can you please post your complete CombineGVCFs
command line, including input file? The input(s) to this tool should have .g.vcf
or .g.vcf.gz
extensions. Can you confirm that your input(s) are actually GVCF files?
Hello,
I have the same problem,
path_input_file=/work/gr-fe/archive/sample_repository/all_exome_gvcfs_hg38/FVH/exomes #patient GVCF path_name_individu=/work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_name.txt path_output=/work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_data.vcf.gz tmp_folder=/scratch/sboutry/logs/combine_gvcf_file nbr_groups=2
REF=/work/gr-fe/saadat/Reference_Genome/GRCH38_no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz BCFTOOLS=/work/gr-fe/sboutry/tools/bcftools/install/bin/bcftools export BCFTOOLS_PLUGINS=/work/gr-fe/sboutry/tools/bcftools/bcftools/plugins TABIX=/work/gr-fe/sboutry/tools/tabix/tabix-0.2.6/tabix GATK=/work/gr-fe/sboutry/tools/gatk/gatk-4.2.2.0/gatk
cd ${path_input_file}
${GATK} --java-options "-Xmx180G -XX:ParallelGCThreads=36" CombineGVCFs -R ${REF} --variant ${path_name_individu} -O ${path_output}/patient_data.g.vcf.gz
where all my files are like this
JL0015.g.vcf.gz JL0016.g.vcf.gz JL0017.g.vcf.gz JL0018.g.vcf.gz JL0019.g.vcf.gz JL0020.g.vcf.gz JL0182.g.vcf.gz JL0183.g.vcf.gz JL0184.g.vcf.gz JL0185.g.vcf.gz JL0186.g.vcf.gz JL0234.g.vcf.gz JL0278.g.vcf.gz JL0412.g.vcf.gz JL0417.g.vcf.gz JL0515.g.vcf.gz
A USER ERROR has occurred: Cannot read file:///work/gr-fe/sboutry/excalibur/input/11_12_23_gvcf_FVH/patient_name.txt because no suitable codecs found
Thanks a lot for any help
Best,
Simon
I just rename the file patient_name.txt patient_name.gvcfs.list
And it worked, in case that can help some
When I use gatk to CombineGVCFs, the following error occurs: "Cannot read file because no suitable codecs found". How can I solve this problem?