I was trying sciclone on my data and it took one day and it was
 "checking input data..."  "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2."  "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2." 10284 sites (of 19026 original sites) are copy number neutral and have adequate depth in all samples 238 sites (of 19026 original sites) were removed because of copy-number alterations 8742 sites (of 19026 original sites) were removed because of inadequate depth 8742 sites (of 19026 original sites) were removed because of copy-number alterations or inadequate depth  "clustering..." Disable overlapping std dev condition kmeans initialization: Tumor.vaf Relapse.vaf 0.554656036649214 0.0234683628795812 0.361785698504027 0.423195796317607 0.0176328924516819 0.0381666242562692 0.579921962920046 0.525048517960602 0.30080528290469 0.0624659469531013 0.392210176923077 0.991532659340647 0.0132568691148545 0.472080169984686 0.997534324719097 0.996064462921345 0.995766899999987 0.434549282777778 0.118433075498615 0.0728657581502769 Using threshold: 0.83666
I stopped the process here, and then I got these messages:
Warning messages: 1: did not converge in 10 iterations 2: Quick-TRANSfer stage steps exceeded maximum (= 514200) 3: Quick-TRANSfer stage steps exceeded maximum (= 514200)
could I some how avoid this? Best Mo
Tagging: Chris Miller
Hi there! It is indeed a WES at 200X, I did a tumor-only variant calling with LoFreq. Mutect2 tumor-only gives me even more variants. I tried puting stringent filters like depth of >200, VAF >10%, SB>30. The number was not significantly reduced! What would you recommend for variant calling? should I go for Pool of healthy individuals to call somatic only? I can not get blood samples .
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This comment belongs under @Chris' answer.
Tumor only means that you will almost certainly not be able to remove all germline mutations. The isown paper will provide some useful guidelines for how you can minimize them though. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0446-9
I also encountered the same problem. I extracted the relevant information needed by sciclone from the vcf file generated from the paired normal tumor data as input, and then the following problem has been encountered. I would like to ask whether a certain screening should be carried out when extracting data from the vcf file? If I need to filter the vcf file, what criteria should I use to filter it? Hope to get your help, thank you very much!