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GATK v184.108.40.206 HaplotypeCaller missing SNP
Hi GATK team,
GATK v4.011.0 haplotype caller is missed to call this SNP.
$java8 -Xmx10g -jar /gatk-220.127.116.11/gatk-package-18.104.22.168-local.jar \ HaplotypeCaller \ -R hg19.fa \ -L Target.bed \ -I sample.markDup.recalibrate.bam \ -A Coverage \ -A MappingQualityRankSumTest \ -A ReadPosRankSumTest \ -A BaseQualityRankSumTest \ -G StandardAnnotation \ --dbsnp hg19_dbSNP138.vcf \ --min-base-quality-score 10 \ --output sample.HaplotypeCaller.snp.indel.vcf \ --stand-call-conf 10 \ --bam-output sample.HaplotypeCaller.bam
I have tried various parameters like (--allow-non-unique-kmers-in-ref, --kmer-size 10, 25, 35 ), but no luck.
All base & mapping qualities of the non-reference bases are looking good.
This is the output of the HaplotypeCaller GVCF.
chr20 62316953 . A . . END=62316953 GT:DP:GQ:MIN_DP:PL 0/0:98:0:98:0,0,416
But GATK v3.2 UnifiedGenotyper have detected this variant and pass the filters.
chr20 62316953 . A G 947.77 PASS ABHet=0.622;AC=1;AF=0.500;AN=2;BaseQRankSum=3.481;DP=98;Dels=0.00;FS=5.289;HaplotypeScore=2.3548;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.022;QD=9.67;ReadPosRankSum=-0.366;SB=-3.310e+02 GT:AD:DP:GQ:PL 0/1:61,37:98:99:976,0,1402
Any idea why this SNP was not called by HC?
Thanks for your help.