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HaplotypeCaller does not call any variant in my targeted sequencing data
I am working with targeted sequencing data and, after align it, I started running HaplotypeCaller to generate gvcf files, using the same line that I used before for exome sequencing analysis (changing the bedfile), which worked correctly. However, with the targeted sequencing data, although there are variant positions when looking at the bamfiles with igv, haplotype caller calls all positions 0/0. Those positions that are clearly variant with igv have PL values of 0,0,0 and calls 0/0, despite being 100% the same alternate allele. Alternate allele in the gvcf file is called .
This is the HaplotypeCaller line:
java -jar /GATK/GenomeAnalysisTK-3.3-0-g37228af/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19/hg19.fasta -I /$IN --dbsnp dbsnp_138.hg19.vcf -o /$INdir/$SAMPLE.haplotype.vcf.gz -L targetedbedfile.bed -A AlleleBalance -A BaseCounts -A BaseQualityRankSumTest -A ChromosomeCounts -A ClippingRankSumTest -A Coverage -A FisherStrand -A GCContent -A GenotypeSummaries -A HaplotypeScore -A HardyWeinberg -A HomopolymerRun -A InbreedingCoeff -A LikelihoodRankSumTest -A LowMQ -A MVLikelihoodRatio -A MappingQualityRankSumTest -A MappingQualityZero -A NBaseCount -A PossibleDeNovo -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A SampleList -A SnpEff -A SpanningDeletions -A StrandOddsRatio -A TandemRepeatAnnotator -A TransmissionDisequilibriumTest -A VariantType -A AlleleBalanceBySample -A AlleleCountBySample -A DepthPerAlleleBySample -A DepthPerSampleHC -A MappingQualityZeroBySample -A StrandBiasBySample --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 >> /users/project/PanCanRisk_005555_no_backup/PanCanRisk_Targeted/Haplotype_annotation.log_file 2>&1
Could you help me with this issue?
Let me know if you need more information.
Thank you very much,