Remove symbolic alleles for REF in a VCF file.

Question

[pmorellmi]

Hi there!

I'm trying to do BQSR on some sheep genomes. I downloaded the known variants from Ensembl and converted the GVF file to VCF using their script. However, once I try to use it to ran GATK 3.5.0 BaseRecalibrator, it propt this message "Cannot tag a symbolic allele as the reference allele". I've looked for "<>" symbols, as they are the markers for symbolic alleles in VCF as far as I've read, but grep didn't found any outside of the header.

Any idea of what could be happening and how can I solve it?

Thank you for your help.

[Pierre Lindenbaum]

what is the exact command line ? what is the output of

grep -v "#" < your.vcf | cut -f 4 | grep -F '<' -m 10

[pmorellmi]

The command for BaseRecalibrator is this:

 java -Xmx16g -jar $GATK_HOME/GenomeAnalysisTK.jar -T BaseRecalibrator \
  -R ref.fa -I in.bam -o cal.tbl  -knownSites var.vcf

And there was no output.

[Pierre Lindenbaum]

isn't there a stack trace in the error message ?

[pmorellmi]

The whole error message is this:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Cannot tag a symbolic allele as the reference allele

[Pierre Lindenbaum]

try with gatk 3.8 ?

[pmorellmi]

Same result, I'm affraid.

[finswimmer]

Let's check if there are lines with other than CATG in the REF column:

$ awk -v FS="\t" -v OFS="\t" '$4 !~ /[CATG]/' input.vcf

[pmorellmi]

Nothing other than the header as output:

##fileformat=VCFv4.1
##fileDate=20190306
##reference=./Oar/Ovis_aries.Oar_v3.1.dna.toplevel.fa
##INFO=<ID=TSA,Number=1,Type=String,Description="A SO term describing the type of sequence_alteration (child term of SO sequence_alteration).">
##INFO=<ID=dbSNP_150,Number=0,Type=Flag,Description="dbSNP_150 membership">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO