Hi all,
I’m writing to you for an issue on vcftools merge tool. I’m trying to performe the merge of two vcf files with bcftools merge, and the tool seems to work; however, when open the resulting merged vfc file, I see the genomic positions, but NO the geniotypes and info related to the specific vcf files;
Hi @Paola_Orsini,
sorry for that question, but you have tried to scroll over to the right in that window. Have to ask this because I do not understand what you’re trying to show with that screenshot.
Cheers,
Wolfgang
The “vcftools merge” command has been known to present various challenges and issues for users attempting to combine multiple VCF files. One common problem that arises is the inconsistency in sample names, leading to errors during the merging process. Additionally, users may encounter difficulties with incompatible file formats or conflicting variants within the VCF files. These issues can result in erroneous merged outputs and incorrect data interpretation, ultimately hindering the accuracy and reliability of downstream analyses. To mitigate these problems, it is crucial for users to carefully review and standardize sample names, ensure compatibility between file formats, and thoroughly assess the quality of variants before executing the merge command. By addressing these potential pitfalls proactively, researchers can enhance the effectiveness and precision of their genetic analyses using vcftools.
