Jingjiao

gender determination

6

hi, The ichorCNA determines that the gender of a sample is female, in fact, the sample is female，my shell is： ``` Rscript /PUBLIC/software/CANCER/Software/R/R3.4.0/lib64/R/library/ichorCNA/scripts/runIchorCNA.R \ --id P10413356170719 \ --WIG P10413356170719.final.wig \...

Frac. CNA Subclonal: 0.99

1

hello --maxFracCNASubclone=MAXFRACCNASUBCLONE Exclude solutions with fraction of subclonal events greater than this value. Default: [0.7] The Frac. CNA Subclonal: 0.99 of my result is 0.99. My window is 1000000, the...

Hi, I called CNV using GenomeSTRiP software, I analyzed the CNV data via plink(v1.07) --gfile command, and in the only results plink.gvar.summary FIELD and VALUE columns , what is the...

hi I run plink v1.07 Association mapping with segmental CNV data: regional tests the EMP1 and EMP2 of every region is 1 my vcf is ``` #CHROM POS ID REF...

hello， I used the following codes to install the mlab in conda python2 env and successfully installed: ```conda activate python2 conda activate python2 pip install numpy pip install scipy pip...

About snp_pileup --pseudo-snps

4

hello~ About the arguments pseudo-snps ,How much should it be appropriate for WGS，WES and targeted cancer gene panels？

LOH determined

4

Hi I run FACETS and get the results: ``` chrom seg num.mark nhet cnlr.median mafR segclust cnlr.median.clust mafR.clust start end cf.em tcn.em lcn.em 1 1 479 79 0.0965351900685901 0.0403774889537343 14...

snp-pileup Segmentation fault

1

hello, when I run sip-up , the Error is Segmentation fault. And there is no output. Usage: snp-pileup vcd-file output tumor_bam normal_bam thank you best~

What does the size of mafR which in cncf explain?

1

hi, In the output cncf file, the column mafR , what does the size of the number mean？Is there a relationship between the size of the number and the imbalance...