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LiftOverVariants throws error on END tag from initial build
I have Build36 GVCF that is generated by command:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -L $interval_build36 -R $build36--genotyping_mode DISCOVERY -ERC GVCF --some_options $sample.recal_reads.bam -o $sample.raw_variants.b36.g.vcf
and I'm trying to do LiftOverVariants to Build37 using command:
java -jar GenomeAnalysisTK.jar -T LiftoverVariants -R $build36 -V $sample.raw_variants.b36.g.vcf -chain b36tob37.chain -dict human_g1k_v37.dict -o $sample.raw_variants.b37.g.vcf
I'm getting an ERROR:
ERROR MESSAGE: Badly formed variant context at location 1:15870; getEnd() was 15904 but this VariantContext contains an END key with value 5767
The Variant giving this error is:
1 5733 . C <NON_REF> . . END=5739 GT:DP:GQ:MIN_DP:PL 0/0:2:3:2:0,3,45
When I checked on UCSC Browser LiftOver tool, I found out that error position 1:15870 is from build37.
And I thought this was counter-intuitive that END tag includes position from build36 but LiftOverVariants throws an error trying to match the build37 position.
Can you please help me out with a workaround?
I only found the post below related to this issue, but it wasn't very helpful