Merge vcf files with bcftools

Question

[j.lunger18]

I'm trying to merge vcf files, all of which were individually merged previously from 3 different callers, one of them being "unifiedGenotyper", which is what the "ug" stands for here in the vcf header. I used the command:

bcftools merge /paht/to/files/*.vcf.gz > all_merged.vcf.gz

I got the following error:

Not ready for type [0]: VAK_ug_AS_MQ at 21497187

I looked at my header for my files and found this line, which seems relevant:

 ##INFO=<ID=VAK_ug_AS_MQ,Number=A,Type=Float,Description="For the caller ug, Allele-specific RMS Mapping Quality">

and my output file is blank.

Any help would be greatly appreciated. THanks!

FOr more info, here is some more of the header, with the one that didn't work at the bottom:

##INFO=<ID=VAK_ug_AS_QD,Number=1,Type=Float,Description="For the caller ug, Allele-specific Variant Confidence/Quality by Depth">
##INFO=<ID=VAK_ug_VAK_split_alleIdx,Number=1,Type=Integer,Description="For the caller ug, Indicates the index of this biallelic line in the set of biallelic lines extracted from the same multiallelic VCF line.">
##INFO=<ID=VAK_ug_BaseQRankSum,Number=1,Type=Float,Description="For the caller ug, Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=VAK_ug_AS_ReadPosRankSum,Number=A,Type=Float,Description="For the caller ug, allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
##INFO=<ID=VAK_ug_MLEAF,Number=A,Type=Float,Description="For the caller ug, Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=VAK_ug_MLEAC,Number=A,Type=Integer,Description="For the caller ug, Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=VAK_ug_MQ,Number=1,Type=Float,Description="For the caller ug, RMS Mapping Quality">
##INFO=<ID=VAK_ug_QD,Number=1,Type=Float,Description="For the caller ug, Variant Confidence/Quality by Depth">
##INFO=<ID=VAK_ug_HaplotypeScore,Number=1,Type=Float,Description="For the caller ug, Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=VAK_ug_AS_MQ,Number=A,Type=Float,Description="For the caller ug, Allele-specific RMS Mapping Quality">

[finswimmer]

Hello,

this one looks similar. Does it help?

• Is there a way to Scan and Correct bad vcf INFO values?

fin swimmer

[j.lunger18]

There was no solution posted for this question.

[finswimmer]

The reason for the issue in the linked post, was that there were variants which has no value for a specific info tag. So in your case look for variants which have a info tag VAK_ug_AS_MQ without a value. If this is the case you have the same issue.

The solution to for the issue is then to replace all VAK_ug_AS_MQ; by VAK_ug_AS_MQ=.;. This can be done with sed:

sed 's/VAK_ug_AS_MQ;/VAK_ug_AS_MQ=\.;/' input.vcf > output.vcf

[Kevin Blighe]

User has opened a new question, here: Fix or remove format tag in .vcf file