One of the most used values for filtering variants in a somatic mutation workflow is the Alternate Allele Frequency for each sample. This field is not always provided directly in the VCF data but don’t worry, VarSeq will automatically calculate the frequency using the provided allelic depth fiel...
We calculates P_Distance as 1 – 0.5*IBS (identity by state) similarity, with IBS defined as the probability that alleles drawn at random from two individuals at the same locus are the same. For clustering, the distance of an individual from itself is set to 0. The calculation is based ...
encoded by a 0 for the REF allele, 1 for the first ALT allele, 2 for the second ALT allele, etc. When there is a single ALT allele (by far the more common case), GT will be either:
Alt allele frequency (AF): the same as MAF File format and special notes: All input files should be compressed (gzip or bgzip). File format should follow post-imputation VCF file from TOMed. Variants in input vcf.gz files should be sorted by position (TOPMed output is already sorted)....
samples with higher levels of HET calls, lower depth, or more variance in b-allele-frequency (ref / (ref + alt )) for het calls. an ancestry prediction based on projection onto the thousand genomes principal components Finally, it will create a new file ped filesceph1463.peddy.pedthat als...
Variant call confidence normalized by depth of sample reads supporting a variant#MQ:表示覆盖序列质量的均方值RMS Mapping Quality#FQ:phred值关于所有样本相似的可能性#AC,AF 和 AN:AC(Allele Count) 表示该Allele的数目;AF(Allele Frequency) 表示Allele的频率; AN(Allele Number) 表示Allele的总数目。对于1...
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ...
Variant call confidence normalized by depth of sample reads supporting a variant #MQ:表示覆盖序列质量的均方值RMS Mapping Quality #FQ:phred值关于所有样本相似的可能性 #AC,AF 和 AN:AC(Allele Count) 表示该Allele的数目;AF(Allele Frequency) 表示Allele的频率; AN(Allele Number) 表示Allele的总数目。
Phred-scaled likelihoods used for DQ calculation"> ##FORMAT=<ID=DQ,Number=1,Type=Float,Description="De novo quality"> ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description...
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