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。 ...
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 ...
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE)...
Allele frequency is defined as the number of times an allele appears over all individuals at that site, divided by the total number of non-missing alleles at that site. --non-ref-af <float> --max-non-ref-af <float> --non-ref-ac <integer> --max-non-ref-ac <integer> --non-ref-...
or on a pattern match. Variants can also be selected based on annotated properties, such as depth of coverage or allele frequency. This is done usingJEXL expressions. Other VCF files can also be used to modify the selection based on concordance or discordance between different callsets (see -...
minimum minor allele frequency (MAF) of sites to be used (default: 0.01) input value needs to be a value between 0.0 and 1.0 -ts/--topsnp number of top SNPs of each phenotype to be summarized (default: 15) after analysis the specified amount of top SNPs from each phenotype will be ...
It uses 2504 thousand genome samples as backgrounds to calibrate the relatedness calculation and to make ancestry predictions. It does this very quickly by sampling, by using C for computationally intensive parts, and by parallelization. If you use peddy, please cite Pedersen and Quinlan, Who’s ...
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...
// set allele frequency and prepare buffer for sorting for (i=-1; rbuf_next(&buf->rbuf,&i) && irec<nbuf; ) { bcf1_t *line = buf->vcf[i].rec; if ( line->n_allele > buf->prune.mac ) { buf->prune.ac = (int*) realloc(buf->prune.ac, line->n_allele*sizeof(*buf...
a reasonable compromise between time wasted on re-calculation and space wasted on a bloated VCF would be to runvcfdo wsafandvcfdo polarizeon a "master" call set and save the result. Then, sinceINFO/AA(ancestral allele) andFORMAT/WSAF(within-sample allele frequency) are invariant to subsett...