【2.8.1】sentieon--call variant

一、说明

1.1 每个算法的用途

The supported algorithms (ALGORITHM) for this command are:

• LocusCollector, Dedup: for the remove duplicates stage.
• Realigner: for the indel realignment stage.
• QualCal: for the base quality recalibration stage.
• MeanQualityByCycle, QualDistribution, GCBias, AlignmentStat,
InsertSizeMetricAlgo, HsMetricAlgo, CoverageMetrics: for the metrics stage
• Genotyper, Haplotyper: for the variant calling stage.
• ReadWriter: used to output the BAM file after base quality recalibration or
merge multiple BAM files.
• VarCal, ApplyVarCal: for the VQSR stage.
• GVCFtyper: for the joint variant calling stage.

• TNsnv, TNhaplotyper: for the tumor-normal or tumor only analysis.

• TNscope: for the tumor-normal somatic and structural variant analysis.

• RNASplitReadsAtJunction: for the stage to split RNA reads at junctions.

• ContaminationAssessment: for identifying cross-sample contamination from
BAM files.
• CollectVCMetrics: for post-variant calling metrics.

二、结果说明

https://support.sentieon.com/appnotes/out_fields/

2.1 TNscope® also populates the FILTER field for the variants.

• PASS ： The variant is confidently a somatic mutation
• alt_allele_in_normal ： The alternate allele is present in the paired normal sample and is unlikely to be a somatic variant
• clustered_events ： Multiple events are present on the same haplotype as the variant which is indicative of a false-positive call
• germline_risk ： There is evidence that the variant is present in the normal sample given that the variant is present in supplied dbSNP VCF and not present in the supplied COSMIC vcf
• homologous_mapping_event ： More than three events are present at this locus in the tumor which is indicate of a false-positive call
• low_t_alt_frac ： The variant is filtered due to a low alternate allele fraction in the tumor sample
• multi_event_alt_allele_in_normal ： Multiple events are present in the tumor sample and the alternate allele appears in the normal sample
• panel_of_normals ： The mutation is observed in at least two samples in the panel of normals
• str_contraction ： The mutation is a contraction of a short tandem repeat
• t_lod_fstar ： The mutation does not have significant support above noise
• triallelic_site ： The mutation occurs at a triallelic site

参考资料

• https://support.sentieon.com/appnotes/out_fields/