samtools
Problems with bcftools merge
Hi, I'm having some problems with bcftools merge. In details, I can't merge three vcf files created with three different variant calling algorithms. Some vcf fields are different, and the code does not give me a clear error; however, when I open the resulting merged file, there are fewer merged samples than expected, and some vcf file are not included. I attached the first lines of the three vcf files. I can't solve this problem. Thank you in advance for your help and time,
Paola sample3.txt sample2.txt sample1.txt
The test files are not valid VCF format. Please provide a tarball for testing, that can be created with something like
tar -czf test.tar.gz input*.vcf
I, I converted vcf into txt files because the vcf format was not supported and I could not upload and attach vcf files. How may I load or send my vcf files? Thank you again.
Paola
Il giorno mar 25 apr 2023 alle ore 17:01 Petr Danecek < @.***> ha scritto:
The test files are not valid VCF format. Please provide a tarball for testing, that can be created with something like
tar -czf test.tgz input*.vcf
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I believe it is supported, only needs to be named as something.tar.gz, as I just tested. I edited the command above to reflect that