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why HaplotypeCaller did not call variants with high alt allele coverage

jchoojchoo Member
edited October 2017 in Ask the GATK team

Hi GATK team,
HC variant calling command:

GenomeAnalysisTK-3.6.jar -T HaplotypeCaller  --dontUseSoftClippedBases -mbq 10 -stand_call_conf 10 -dt NONE -R hs37d5.fa -I UM1.recal.bam -L test.bed  -D dbsnp147_GRCH37_All_20160601.vcf -o normal.g.vcf -forceActive -ERC GVCF -disableOptimizations

the region in test.bed is :

2   211513107   211513324

below is the screen shot of IGV:

the bam file in the screen shot from up to bottom are:
1, bamout file from GATK using bamOUT option,
2, the bam file after softlipping( soft clip primer region), and BQSR
3, the bam file mapped using bwa-mem

As we can see, most of the reads carry T allele in the position "2:211513118" with high mapping quality and high base quality, but this variants are not called in any mode of HC.

And if we use UG to call this region, this variants were successfully called:

2   211513118   rs4673540   C   T   25161.77    .   AC=2;AF=1.00;AN=2;BaseQRankSum=4.561;DB;DP=691;Dels=0.00;ExcessHet=3.0103;FS=0.000;HaplotypeScore=23.2440;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.000;QD=34.24;ReadPosRankSum=0.000;SOR=11.687    GT:AD:DP:GQ:PL  1/1:1,689:691:99:25190,2045,0 

Any idea why this site was not call using HC?

Thanks

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