20. GcBiasMetrics: *
GcBiasSummaryMetrics: High level metrics that capture how biad the coverage in a certain lane is.*
GenotypeConcordanceContingencyMetrics: Class that holds metrics about the Genotype Concordance contingency tables.* GenotypeConcordanceDetailMetrics: Class that holds detail metrics about Genotype Concordance*
GenotypeConcordanceSummaryMetrics: Class that holds summary metrics about Genotype Concordance*
教育部考试中心雅思HsMetrics:
Metrics generated by CollectHsMetrics for the analysis of target-capture quencing experiments.
IlluminaBacallingMetrics: Metric for Illumina Bacalling that stores means and standard deviations on a per-barcode per-lane basis.*
IlluminaLaneMetrics: Embodies characteristics that describe a lane.*
IlluminaPhasingMetrics: Metrics for Illumina Bacalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.*zoom怎么读
IndependentReplicateMetric: A class to store information relevant for biological rate estimation*
InrtSizeMetrics: Metrics about the inrt size distribution of a paired-end library, created by the
CollectInrtSizeMetrics program and usually written to a file with the extension ".inrt_size_metrics".*
JumpingLibraryMetrics: High level metrics about the prence of outward- and inward-facing pairs within a SAM file
generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".*
MendelianViolationMetrics: Describes the type and number of mendelian violations found within a Trio.*
paeMergeableMetricBa: An extension of MetricBa that knows how to merge-by-adding fields that are appropriately annotated.*
MultilevelMetrics: *
RnaSeqMetrics: Metrics about the alignment of RNA-q reads within a SAM file to genes, produced by the
katy perry roar
CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".*
RrbsCpgDetailMetrics: Holds information about CpG sites encountered for RRBS processing QC*
RrbsSummaryMetrics: Holds summary statistics from RRBS processing QC*
SequencingArtifactMetrics.BaitBiasDetailMetrics: Bait bias artifacts broken down by context.*
准考证号查询网
SequencingArtifactMetrics.BaitBiasSummaryMetrics: Summary analysis of a single bait bias artifact, also known as a reference bias artifact.*
SequencingArtifactMetrics.PreAdapterDetailMetrics: Pre-adapter artifacts broken down by context.*
SequencingArtifactMetrics.PreAdapterSummaryMetrics: Summary analysis of a single pre-adapter artifact.*
TargetedPcrMetrics: Metrics class for the analysis of reads obtained from targeted pcr *
自主招生成绩UmiMetrics: Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
详细功能
Co llec tH sMetr ic s:
分析靶向测序（hybr id-lec tio n）的相关指标
该命令读取SAM/BAM⽂件。HS（杂交捕获，靶向测序，hybrid-lection）是靶向测序常⽤的技术，如外显⼦靶向测序，更多信息参考GATK Dictionary entry.
1。
hs_library_size：被捕获的⽂库⽚段数量估计值
hs_penalty_10x：80% 靶向区区域碱基达到 10X时的捕获罚分。即：当设计10M的靶向区域时，要得到 10X coverage， 需要测序，直到PF_ALIGNED_BASES =10^7 * 10 * HS_PENALTY_10X.
hs_penalty_20x：想要80%区域到达 20X coverage。
转圜
hs_penalty_30x
hs_penalty_40x
hs_penalty_50x
hs_penalty_100x
3）target 覆盖度评估，评估下游分析中的可靠性。⽐如target 区域平均覆盖度，不同覆盖度⽔平的碱基⽐例，不同条件过滤的碱基⽐例。按照所有条件过滤后计算这些指标。
mean_bait_coverage：所有 bait 位点上的平均覆盖度。
pct_usable_bas_on_bait： 可使⽤的 PF 碱基中，⽐对到 bait 上的去重的碱基数量。
pct_usable_bas_on_target： 可使⽤的 PF 碱基中，⽐对到 target 上的去重的碱基数量。
fold_enrichment：扩增区域被扩增的倍数
mean_target_coverage： target 区域平均覆盖度。
median_target_coverage：覆盖度
independenceday
max_target_coverage：覆盖度
min_target_coverage：覆盖度
vanilla hzero_cvg_targets_pct：target 区域覆盖度<1的⽐例。
不同条件过滤的碱基⽐例：
pct_exc_dupe：标记为重复的 reads 。
pct_exc_adapter：adapter
pct_exc_mapq：低⽐对质量
pct_exc_baq： 低碱基碱基。
pct_exc_overlap： 重复序列⽐例。 the cond obrvation from an inrt with overlapping reads.
pct_exc_off_target： ⽐对到 taget 区域外。
不同覆盖度⽔平的碱基⽐例：
pct_target_bas_1x：⽐对到target 区域的，不⼩于 1X的碱基⽐例
pct_target_bas_2x
pct_target_bas_10x
pct_target_bas_20x
pct_target_bas_30x
pct_target_bas_40x
growl是什么意思
pct_target_bas_50x
pct_target_bas_100x
at_dropout：与平均覆盖度相⽐，低碱基含量（GC<50%）的区域，偏低的程度。结果是个⽐值，表⽰总reads中⽐对到 低 GC含量区域的⽐例。
gc_dropout：⾼ GC含量的区域上 reads ⽐例。
het_snp_nsitivity：HET SNP 理论值。
het_snp_q：HET SNP 理论值的 Q 值，
sample
library
read_group
