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HaplotypeCaller report different genotype on the same location with different setting of -L

yanarkiay01yanarkiay01 HoustonMember
edited April 2015 in Ask the GATK team

Hi GATK team,

I am using the GATK 3.3 HaplotypeCaller. I found if i use different -L i will have different genotype on the same location. My para is very simple: -T HaplotypeCaller -R ucsc.hg19.fasta -mbq 20 --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -I test.bam -L chr17 -o output.vcf

I check the same site.
If i set -L chr17:36070200-36071000, there is a reported SNV.
if i set -L chr17:36000000-36140000, there is no SNV report.
if i set larger: -L chr17:30000000-40000000, it just show up again.
if i use the whole chr17, it gone.

This is very confusing me. it is a C->G variant at chr17. The snp is looks like:
GT 0/1
AB 0.84
AD 257,49,0
DP 306
GQ 99
PGT 0|1
PL 2966,0,10470,3755,10800,14555
SB 14,243,49,0

While I checked the bam file with IGV. There are two wired things: (1) there is no read supporting the non-reference allele. (2) the depth is about 600, far more deeper than the HaplotypeCaller reported. Why would this happen?



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