REQUIRED for all errors and issues:
Hello, I'm doing a panel of normals (PON) and I'm having a problem. Apparently caused because differents files have the same name of the tumor sample.
a) GATK version used: 22.214.171.124
b) Exact command used:
gatk GenomicsDBImport -R Homo_sapiens_assembly19.fasta --genomicsdb-workspace-path pon_db -V 4666_1.vcf.gz -V 4672_2.vcf.gz -V 4732_8.vcf.gz -V 4862_2.vcf.gz -V 4862_3.vcf.gz -V 4862_4.vcf.gz -V 4862_5.vcf.gz -V 4862_6.vcf.gz -V 4862_7.vcf.gz -V 4862_8.vcf.gz -V 4886_5.vcf.gz -V 4886_6.vcf.gz -V 4886_7.vcf.gz -V 4886_8.vcf.gz -V 4902_1.vcf.gz -V 4902_2.vcf.gz -V 4902_3.vcf.gz -V 4902_4.vcf.gz -V 4902_5.vcf.gz -V 4902_6.vcf.gz -V 4902_7.vcf.gz -V 4902_8.vcf.gz -V 4943_1.vcf.gz -V 4943_2.vcf.gz -V 4943_3.vcf.gz -V 4943_4.vcf.gz -V 4943_5.vcf.gz -V 4943_7.vcf.gz -V 4943_8.vcf.gz -V 4988_1.vcf.gz -V 4988_2.vcf.gz -V 4988_3.vcf.gz -V 4988_4.vcf.gz -V 5043_1.vcf.gz -V 5043_2.vcf.gz -V 5043_3.vcf.gz -V 5043_4.vcf.gz -V 5043_5.vcf.gz -V 5043_6.vcf.gz -V 5043_7.vcf.gz -V 5043_8.vcf.gz -V 5051_1.vcf.gz -V 5051_2.vcf.gz -V 5051_3.vcf.gz -V 5051_4.vcf.gz -V 5051_5.vcf.gz -V 5051_6.vcf.gz -V 5051_7.vcf.gz -V 5051_8.vcf.gz -V 5090_1.vcf.gz -V 5090_2.vcf.gz -V 5090_3.vcf.gz -V 5090_4.vcf.gz -V 5090_5.vcf.gz -V 5090_6.vcf.gz -V 5090_7.vcf.gz -V 5090_8.vcf.gz -V 5105_1.vcf.gz -V 5105_2.vcf.gz -V 5105_3.vcf.gz -V 5105_4.vcf.gz -V 5105_5.vcf.gz -V 5105_6.vcf.gz -V 5105_7.vcf.gz -V 5105_8.vcf.gz
c) Entire program log:
A USER ERROR has occurred: Duplicate sample: PD4086bv2. Sample was found in both file:///home/adrianib/gatk-126.96.36.199/Genome_Analyzer_II/4862_2.vcf.gz and 4672_2.vcf.gz.
When I saw this error, I decompressed the file, oppeden and change the name "PD4086bv2" in one of the files (4672_2.vcf). After that, I save the changes and compressed the file again.
Then, I proceed to run the command of the letter b) one more time, but I have another error:
A USER ERROR has occurred: Failed to create reader from file:///home/adrianib/gatk-188.8.131.52/Genome_Analyzer_II/4672_2.vcf.gz because of the following error:
Unable to parse header with error: Invalid GZIP header, for input source: file:///home/adrianib/gatk-184.108.40.206/Genome_Analyzer_II/4672_2.vcf.gz
So, I'm lost since here. How can I fix this error and create my PON?
Thank you in advance.
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