EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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EVA-1256 Report duplicate samples #168

Closed jmmut closed 5 years ago

jmmut commented 5 years ago

Example output:

$ ./bin/vcf_validator -i ../../test/input_files/v4.3/failed/failed_body_sample_011.vcf -o /tmp
[info] Reading from input file...
[info] Summary report written to : /tmp/failed_body_sample_011.vcf.errors_summary.1537521390924.txt
[info] According to the VCF specification, the input file is not valid

$ cat /tmp/failed_body_sample_011.vcf.errors_summary.1537521390924.txt
According to the VCF specification, the input file is not valid
Error: The header line has 3 repeated sample names: [HG00096, HG00097, HG00096]. This occurs 1 time(s), first time in line 3.
Warning: A valid 'reference' entry is not listed in the meta section. This occurs 1 time(s), first time in line 4.
Warning: Chromosome/contig '1' is not described in a 'contig' meta description. This occurs 1 time(s), first time in line 4.