vcf_operations.cpp:525 Sample names are not unique

[xuefenfei712]

Dear Hannes

I am using Graphtyper to call SNPs, it is quite convinent, while I got the error below

vcf_operations.cpp:525 Sample names are not unique. The output VCF file will contain duplicated sample names (which is against the VCF specs).

I double checked mu header of bamfiles, they are unique, could you tell me how to deal with it? because later I cannot merge them together because of this issue.

Thankyou

xue

[hannespetur]

Hi. Could you have a closer look at the sample names in the VCF header and check if the names have been parsed incorrectly somehow compared to the BAMs?

Alternatively, you could take as input a list of paths that are symlinks similar to /....../<SAMPLE_NAME>.bam and use the graphtyper genotype option --get_sample_names_from_filename to ignore the BAM headers and use the filenames instead.