How to force merge a VCF files, for different samples?
I obtained vcf files from a tool I used. I want to merge them but it was missing some TAG info, which I fixed. Now, I am having somekind of ERROR probably emerging again from HEADER.
Is there a way to force merge vcf files, if not fix the vcf files. I don't really care much about HEADER at this time.
Thanks,
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kirannbishwa01
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Bcftools has subcommands merge and annotate VCF files.
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So you used some tool, on some data generated with a technology on some samples, and got vcf files.
You were missing some tag info, which you somehow fixed.
And now, using an unknown tool, you get an error.
You need to add a lot of information to this question. I'm considering closing this because you are just making it impossible to answer.
Hi @WouterDeCoster.
How are you doing? Yeah, I used a a toold called phase to phase my variants, which unfortunately in the recent version had a bug and didn't add
PGtag in the header. I have to merge different vcf files that came out of this tool, but I am getting error on every tool that does vcf merge.I also tried adding PG field using AWK, sed but no luck excepting the error.
I think rest of the DATA on VCF files are good, and I need to do some presentation using this data. I don't have much time to redo the whole analyses (phasing) and I think force-merging the VCF would be all fine. What I am saying is HEADER information is least of the concern for what I am doing, but all the VCF merge tools are complaining about error somewhere in HEADER. I also don't have much time to fix that bug as of right now.
I think the best option for right now, is just merge the VCF files (different samples), without any complex manipuation.