...并这些gvcf文件，但是提示我错误：A USER ERROR has occurred: The list of input alleles must contain <NON_REF> as an allele but that is not the case at position 763769; please use the Haplotype Caller with gVCF output to generate appropriate records。由于缺乏bam文件我只能...
...sums checked** using staged installationconfigure: units: 0.8-2checking whether the C++ compiler works... yeschecking for C++ compiler default output file name... a.outchecking for suffix of executables...checking whether we are cross compiling... nochecking for suffix of object files... ochecking w...
traitColors = numbers2colors(datTraits, signed = FALSE)
Warning message:
In numbers2colors(datTraits, signed = FALSE) :
(some columns in) 'x' are constant. Their color will be the color of NA.
> # Plot the sample dendrogram and the colors underneath.
...per-read quality flag (Read_Filter), and removing base quality scores from the file. In the resulting files, all reads have a Read_Filter flag with value pass or reject. Importantly, it is still possible to produce fastq formatted files from SRA Lite format using the SRA toolkit. In this case, each ...
...能出现链偏好性。MLEAC：Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listedMLEAF：Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT al...
...例文件，放了所有样品的集合，但是跑出来是如下这样
the Number of subPop samples[found in VCF] is 0
sub Group Population szie is too small, SubGroup sample size: 0
##begin pair-wise R^2 cal. after filter Remain SNP Number : 0
#% number bin is 11%......--&...
...脚本中提到了，所生成的三种文件，其中 clip graph: This is the default graph. Stretches of sequence >10kb that were not aligned to the underlying SV/minigraph are removed. "Dangling" nodes (ie that don't have an edge on each side) that aren't on the reference path are also removed...