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
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