Hi GATK team,
First I'd like to thank you guys for the tools that you're making available for the community!
The problem is that I have run my sample using Haplotype Caller and I faced some missing variants when I ran the HaplotypeCaller running with nct.
How I figured out ?
2) When I ran with the command (with nct deactivated):
java -Xmx10g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta -I 165019-0-LAOM-N10_26_001_L001_1.realigned.recal.bam --dbsnp dbsnp_138.hg19.vcf -T HaplotypeCaller -stand_emit_conf 30.0 -stand_call_conf 30.0 -dcov 5000 --genotyping_mode DISCOVERY -A FisherStrand -A AlleleBalance -A BaseCounts -A StrandOddsRatio -A StrandBiasBySample --max_alternate_alleles 3 -o .165019-0-LAOM-N10_26_001_L001_1.realigned.recal.gatk.high.vcf -L NUTRI.list
chr12 48239835 rs1544410 C T 6129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=11.887;DB;DP=509;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSu
m=1.141;QD=12.04;ReadPosRankSum=0.418;SOR=0.640 GT:AD:GQ:PL:SB 0/1:261,247:99:6158,0,6273:261,0,247,0
1) When I ran with the command below (with nct activated) :
java -Xmx10g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta -nct 8 -I 165019-0-LAOM-N10_26_001_L001_1.realigned.recal.bam --dbsnp dbsnp_138.hg19.vcf -T HaplotypeCaller -stand_emit_conf 30.0 -stand_call_conf 30.0 -dcov 5000 --genotyping_mode DISCOVERY -A FisherStrand -A AlleleBalance -A BaseCounts -A StrandOddsRatio -A StrandBiasBySample --max_alternate_alleles 3 -o .165019-0-LAOM-N10_26_001_L001_1.realigned.recal.gatk.high.vcf -L NUTRI.list
The variant above is missing from my vcf (it's not called).
Checked the flags: DP = 509 (good depth); QD 12.04 > 2.0;
I have ran with the bamout option to see the variant with HaplotypeCaller and it shows the variant as you can see at the figure below.
This is the original bam as INPUT at my variant caller
My HaplotypeCaller is running at version 3.3.
PS: I have seen some threads at the forum about missing variants running with nct, is is correct?