jiangyulab / cnvcaller Goto Github PK

Hello,

I found a lot of abnormal values in my genotypeCNVR.vcf.

END=1439200;SVTYPE=DUP;SILHOUETTESCORE=nan;CALINSKIHARABAZESCORE=nan;LOGLIKELIHOOD=2.55971620969 GT:CP 0/1:2.58 0/1:3.46 0/1:2.74

Do I need to filter out these CNVR?

很高兴使用您的CNV检测软件，但我运行到第二步Individual.Process.sh，缺乏link文件，但是在教程中该链接失效了，是否可以提供给我新的地址，谢谢您~
pig

Hello teacher, when I used the Individual.Process.sh script to analyze bam files, files in RD_normalized folder in three folders were blank in the final output result. Could you please tell me the reason? Bash Individual. Process.
Sh - b/home/wangb / 30 WGS/bam/DBS5 sorted. Uniqe. Rg. Dedup. Bam - h DBS5 - d Btau5.0.1 _800_link -s
This is my input code.

Hi,

I found many Heterozygous Genotype in vcf file like 0/1 1/2 0/2. How to understand Heterozygous copy?

Best,
Kun

-r|--pearsonCorrelation minimum of Pearson’s correlation coefficient between the two adjacent non-overlapping windows
0.5 for sample size (0, 30]
0.4 for sample size (30, 50]
0.3 for sample size (50, 100]
0.2 for sample size (100, 200]
0.15 for sample size (200, 500]
0.1 for sample size (500,+∞)
I cant really get the point，I thought

I recently tried to run Genotype.py for changing my mergeCNVR file to vcf, but problem occured:(see below)
Traceback (most recent call last):
File "/home/liujf/WORKSPACE/huangqq/Mysoftware/CNVcaller-master/Genotype.py", line 210, in
main()
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/liujf/WORKSPACE/huangqq/Mysoftware/CNVcaller-master/Genotype.py", line 193, in main
gtdf = pd.DataFrame(genotype(cnvays))
File "/home/liujf/WORKSPACE/huangqq/Mysoftware/CNVcaller-master/Genotype.py", line 43, in genotype
tol=1e-3, covariance_type='full').fit(cnv)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/sklearn/mixture/_base.py", line 192, in fit
self.fit_predict(X, y)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/sklearn/mixture/_base.py", line 219, in fit_predict
X = _check_X(X, self.n_components, ensure_min_samples=2)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/sklearn/mixture/_base.py", line 53, in _check_X
ensure_min_samples=ensure_min_samples)
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/sklearn/utils/validation.py", line 578, in check_array
allow_nan=force_all_finite == 'allow-nan')
File "/home/liujf/WORKSPACE/liwn/Mysoftware/anaconda3/lib/python3.7/site-packages/sklearn/utils/validation.py", line 60, in _assert_all_finite
msg_dtype if msg_dtype is not None else X.dtype)
ValueError: Input contains NaN, infinity or a value too large for dtype('float64').
Could you help me solve this problem? I will be really grateful!

Hi ~
Thanks for developing this handy program.
I am working on a haploid fungus and wondering if I can use this program as well.
I have 12 samples and generate these two files at last. It seems like all the sample was assumed as diploid by default which can also be seen in the VCF file. Any suggestions?
I also analyzed the mitochondria at the same time. Will it influence the results as the mitochondrial genome usually has very high coverage? Is it recommended to run the nuclear genome and the mitochondrial genome separately?
Last, I got lots of warnings like this miniconda3/envs/mitozEnv/lib/python3.7/site-packages/sklearn/cluster/k_means_.py:968: ConvergenceWarning: Number of distinct clusters (8) found smaller than n_clusters (10). Possibly due to duplicate points in X. return_n_iter=True) Any suggestions to solve them?
Thank you very much!

genotypeCNVR.vcf.zip
genotypeCNVR.tsv.zip

Hi,

I find there are a lot of CN0s in my result, which means many samples do not have the specific contigs in their genomes. It makes me so confused. Why do they have so many deletions in their genomes? Could it be the competitive regions in the genomes that make some reads map to somewhere else? Please advise. Thank you very much!
mergeCNVR.zip

how can I comprehend the genotype like 0/1|1/1|0/2|2/3…and how about the A、B、C in the tsv result？
how can I filter the sites by SILHOUETTESCORE & CALINSKIHARABAZESCORE&LOGLIKELIHOOD, are there any recommanded threshholds?
how to define the heterozygousity of a CNVsite for single individual?

sorry to bother you, when I run CNV.Discovery.sh, it reminds me that the file "1500_mean_20.00_SD_29.48_sex_1" not find, I don't understand why.

Use of uninitialized value $sd in numeric gt (>) at 2.1.CNVDiscoveryMerge.pl line 72, line 67.
0.136449659348978
/RD_normalized/1500_mean_20.00_SD_29.48_sex_1 0.35
/RD_normalized/1500_mean_20.00_SD_29.48_sex_1 file not found
length() used on @tmp_start_array (did you mean "scalar(@tmp_start_array)"?) at CNVcaller/bin/2.2.CNVRRedundancy.pl line 48.
length() used on @tmp (did you mean "scalar(@tmp)"?) at CNVcaller/bin/2.2.CNVRRedundancy.pl line 48
Error: cannot read primaryCNVR file primaryCNVR.

Hi, teacher
Do we need to remove duplication reads from the input BAM file before call CNV?

Hello,

Could you please help me with the following issue? What can be a reason for this error when running CNV.Discovery.sh?

Use of uninitialized value $sd in numeric gt (>) at /CNVcaller/bin/2.1.CNVDiscoveryMerge.pl line 72, line 10.
2.1179679144385

Where should I look for a root cause?

Thank you for sharing your software!

[E::hts_open_format] fail to open file 'SRR5149617_RGSM.bam'
samtools view: failed to open "SRR5149617_RGSM.bam" for reading: No such file or directory
Unexpected bam format...

I've met an issue that to do GWAS with CNVcaller results. My samples' numeric pheon dont have classic case/control differentiation, and I have no idea to transformed genotype to a similar biallelic geno data. Says, I cant make to finish assoc analysis with a proper software. I need some help.