Merging VCF files with updated INFO tags

Question

[MAPK]

I have multiple vcf files with different samples. I want to merge them with updated INFO tags, especially AC fields. I have tried the following command below, but it does not work. Please suggest how I can execute the command.

bcftools merge -i AC:sum fileA.vcf.gz fileB.vcf.gz  -O v -o merged.vcf

[MAPK]

I desperately need to use this. Please help.

[DG]

What sort of error or unexpected output are you getting? I believe you need to move the -O and -o flags to before fileA.vcf.gz and fileB.vcf.gz for one thing, in order to fit with the proper execution of the program (bcftools merge [options] [files])

[MAPK]

Hi Dan, I was able to merge the files, but the values in AC tag were not updated in the merged files. I could not use the -i option to get the updated AC values.

[DG]

That I'm not sure unfortunately. I don't typically use bcftools. Is it pulling AC values from just one file versus summing them?

[MAPK]

That is right. What do you use to merge two vcf files?

[DG]

For merging multiple samples into the same VCF file I've typically used GATK's CombineVariants in the past, but usually now I do multi-sample calling. For my current workflows I usually just need to merge VCF's that are from the same sample. I've been using a mix of bcbio-ensemble's merge method and some custom scripts.