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bcftools - issue when trying to merge two VCFs #1685
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That's indeed a very cryptic message, did not expect to ever encounter such case. Could you please check the headers and show which the tags are defined as Number=G/A/R? A small test case to reproduce the problem would be really helpful here. |
I've uploaded the original files to OneDrive! These are the commands that I used: The tags that are defined as Number=A are: I hope these are what you're looking for. Thanks again for your kind help! |
Thank you for the test files. The problem is caused by flag types being defined as
An easy workaround should be to fix the header
Ideally the program that produced the VCFs should be fixed. |
Invalid definitions are fixed internally and warning such as [W::bcf_hdr_register_hrec] The definition of Flag "INFO/SNP" is invalid, forcing Number=0 are printed so that downstream analyses can work (e.g. `bcftools merge`). However, output VCF headers are not fixed. This could go one step further and also modify the headers. See also samtools/bcftools#1685
After this pull request is fixed samtools/htslib#1415, bcftools will be able to work with such files. Note that it is only a workaround, this should really be addressed at the VCF producer side. |
Invalid definitions are fixed internally and warning such as [W::bcf_hdr_register_hrec] The definition of Flag "INFO/SNP" is invalid, forcing Number=0 are printed so that downstream analyses can work (e.g. `bcftools merge`). However, output VCF headers are not fixed. This could go one step further and also modify the headers. See also samtools/bcftools#1685
This is now merged via samtools/htslib#1415 |
Invalid definitions are fixed internally and warning such as [W::bcf_hdr_register_hrec] The definition of Flag "INFO/SNP" is invalid, forcing Number=0 are printed so that downstream analyses can work (e.g. `bcftools merge`). However, output VCF headers are not fixed. This could go one step further and also modify the headers. See also samtools/bcftools#1685
I'm getting this error when trying to merge my two VCF files. I first used bgzip to compress my files and then indexed them before merging.
Not ready for type [0]: SNP at 82113
Thanks for helping!
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