We are trying to call SNPs from a bam file by using GATK 4.1 HaplotypeCaller. This bam file was sorted and read groups were added. Unfortunately, we are getting error : " Badly formed variant context at location 21:10945870; getEnd() was 10945870 but this VariantContext contains an END key with value 10990763 ". Here our code:
..../gatk --java-options "-Xmx25g" HaplotypeCaller -I xxx.bam -R yyy.fa -L ..../1000G_chr21.bed --output-mode EMIT_ALL_SITES --genotyping-mode GENOTYPE_GIVEN_ALLELES --alleles zzz.vcf --output kkk.vcf
The same file was used for SNP calling before with GATK 3.2 UnifiedGenotyper. It worked successfully. There wasn't any error like that. The input file and 1000G bed file were validated via ValidateSamFile. They are valid. We tried to find the position (21:10945870) , but there is no such position neither in input file nor in bed file. We couldn't find any solution. What could be the reason for that? Any suggestions?