Question: Sciclone took too long
1
gravatar for sm.hashemin
12 weeks ago by
sm.hashemin60
sm.hashemin60 wrote:

Dear Chris,

I was trying sciclone on my data and it took one day and it was

    [1] "checking input data..."
    [1] "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2."
    [1] "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
    [1] "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

sciclone • 218 views
ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by sm.hashemin60
1

Tagging: Chris Miller

ADD REPLYlink written 12 weeks ago by genomax54k

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 .

Best Mo

ADD REPLYlink written 11 weeks ago by sm.hashemin60
1

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @Chris' answer.

ADD REPLYlink written 11 weeks ago by genomax54k

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

ADD REPLYlink written 11 weeks ago by Chris Miller20k
1
gravatar for Chris Miller
12 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Are your 19k sites from exome or WGS? If the former, I suspect that something has gone horribly wrong with your mutation calling. In a decade of working on tumors, I've only seen a handful of MMR/POLE deficient cases with that kind of mutational burden in an exome.

Sciclone will also take a long time if your data is very noisy. Do a simple X/Y plot of your VAF data and see if you can make out the clusters by eye. If not, then the algorithm is likely going to have a hard time too. You might consider being more stringent with your variant calling parameters and requiring a higher minimum depth to tighten things up.

ADD COMMENTlink written 12 weeks ago by Chris Miller20k
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