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sanger confirmed SNV present with HaplotypeCaller 2.7, absent with HaplotypeCaller 3.3

ano1986ano1986 BelgiumMember

We performed variant calling on a whole-exome sequenced human internal control sample. We have a set of 60 confirmed Sanger sequencing SNVs for this sample, which are all detected when we use HaplotypeCaller 2.7 with the following parameters:

-T HaplotypeCaller -nct 8 -R hg19_chr1-y.fasta -I input.bam --genotyping_mode DISCOVERY --max_alternate_alleles 12 --dbsnp dbsnp_137.hg19.vcf --disable_auto_index_creation_and_locking_when_reading_rods -et NO_ET -stand_call_conf 30.0 -stand_emit_conf 15.0 -o output.vcf -dcov 900

When we start from the same .bam file but using HaplotypeCaller 3.3 with the same parameters:

-T HaplotypeCaller -nct 8 -R hg19_chr1-y.fasta -I input.bam --genotyping_mode DISCOVERY --max_alternate_alleles 12 --dbsnp dbsnp_137.hg19.vcf --disable_auto_index_creation_and_locking_when_reading_rods -et NO_ET -stand_call_conf 30.0 -stand_emit_conf 15.0 -o output.vcf -dcov 900

one SNV is not detected (chr19:49671151). I've attached a printscreen of IGV (first track: original .bam file, second track --bamout for hc2.7, third track is --bamout hc3.3). All quality scores look normal. I can provide you with the .bam files if needed.

Could you recommend some things that I can check to find out why this confirmed variant is not detected with hc3.3?

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