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LiftoverVCF; mismatching reference alleles after lift over

Hi,

I am running LiftoverVCF from gatk-4.0.8.1 to convert my VCF from hg18 to hg19.

Here is my command:

/apps/well/java/jdk1.8.0_172/bin/java -jar /users/mcvean/tutert/gatk-4.0.8.1/gatk-package-4.0.8.1-local.jar LiftoverVcf -I /users/mcvean/tutert/58BC_affy_all.with_chr.vcf -O /users/mcvean/tutert/liftedover.vcf -CHAIN /users/mcvean/tutert/hg18ToHg19.over.chain -REJECT /users/mcvean/tutert/rejected.vcf -R /users/mcvean/tutert/ucsc.hg19.fasta -RECOVER_SWAPPED_REF_ALT true --MAX_RECORDS_IN_RAM 100000 -

However in my output log I see this:
303130 variants lifted over but had mismatching reference alleles after lift over.
42.2971% of variants were not successfully lifted over and written to the output.

I believe this is an alt/ref mismatch problem still (since I looked at the snps in the output rejected file and they were all both in hg18/hg19 but just differed by this mismatch).

Could someone please help me with this?

Answers

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