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Spurious insertions being called by HaplotypeCaller?
I just called variants from the same bwa-generated bam file using 1) samtools/bcftools and 2) HaplotypeCaller.
Downstream analysis indicated that a particular locus looked interesting, but only in the GATK output. When I looked up the position in the vcf files, the samtools vcf file showed no variant at this position while the GATK vcf file showed a single nucleotide insertion.
Viewing the bam file in IGV shows no insertion at this site and very good read depth (>100x) and mapping quality. There is an insertion 10nt away
Is there anything known that might cause such behavior? Are there any parameters in HaplotypeCaller that might make insertion assignments more likely?