bcftools merge fails: Only fixed-length vectors are supported

Question: bcftools merge fails: Only fixed-length vectors are supported

10 months ago by

Tübingen

Dear community members,

I face a problem - I need to create a multi-sample VCF from thousands of VCF files, the problem is - they are created with FreeBayes and somehow the techniques I always use do not work. E.g. when I try to use

bcftools merge

it tells me:

Only fixed-length vectors are supported with -i sum:DP

I am not that proficient with VCF format and this error message is totally cryptic for me - do you have an idea why it may happen? An example line from my VCF files looks like:

chr1    911595  .       A       G       2911    .       MQM=60  GT:DP:AO        1/1:93:93

I had an idea that it may be caused by multi-allelic sites - but bcftools in theory should be able to deal with them...

Any advice on how to create a multi-sample VCF is appreciated! (I used bcftools merge several times with GATK output and it worked, but now I am stuck...)

Googling did not help.

Command line used:

/mnt/share/opt/bcftools-1.9/bcftools merge sample1.vcf.gz  sample2.vcf.gz --merge none > merged.cases.vcf

bcftools mutli-sample vcf • 270 views

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modified 10 months ago by Carambakaracho • 2.3k • written 10 months ago by German.M.Demidov • 1.9k

10 months ago by

Carambakaracho • 2.3k

Germany/Cologne

Carambakaracho • 2.3k wrote:

As you don't have DP values in the info column, switch of default behaviour to sum up the DP values in the infocolumn

bcftools merge -i -

This is untested but that's how I understand the help:

bcftools merge --help
   -i, --info-rules <tag:method,..>   rules for merging INFO fields (method is one of sum,avg,min,max,join) or "-" to turn off the default [DP:sum,DP4:sum]

ADD COMMENT • link modified 10 months ago • written 10 months ago by Carambakaracho • 2.3k

Thanks I will try! I honestly checked the manual but somehow my logic was not efficient enough to find this...