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stat-lab / EvalSVcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers
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VCF conversion fails for CNVnator and Manta #6

Closed bioinfo89 closed 4 years ago

bioinfo89 commented 4 years ago

Hi,

I am using the convert_SV_callers_vcf.pl for Delly, Lumpy, Manta and CNVnator output files (All VCFs). It works fine for Delly and Lumpy VCF files but I don't get any output for Manta (diploid VCF) and CNVnator files, the files are empty and there is no error message also while running it.

I am not sure what went wrong. Any help would be appreciated.

stat-lab commented 4 years ago

I uploaded a fixed script of ‘convert_CNVnator_vcf.pl’, which had contained a wrong path of the gap.bed file. But I’m not sure why the Manta conversion did not go well. Have you used a diploidSV.vcf.gz file for the Manta output? If you so, could you send it to me?

2020/08/03 8:26、bioinfo89 notifications@github.comのメール:

Hi,

I am using the convert_SV_callers_vcf.pl for Delly, Lumpy, Manta and CNVnator output files (All VCFs). It works fine for Delly and Lumpy VCF files but I don't get any output for Manta (diploid VCF) and CNVnator files, the files are empty and there is no error message also while running it.

I am not sure what went wrong. Any help would be appreciated.

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bioinfo89 commented 4 years ago

I did change the path to gap.bed in the CNVnator script before using it. Yes, I used diploidSV.vcf.gz file as input. Sending you Manta files via email.

Thanks!

stat-lab commented 4 years ago

The problem was attributed to the reference chromosome names based on the hg19 reference, which has 'chr' prefix in the chromosome names. This evaluation system has been developed with the GRCh37 reference. I changed all the scripts so that the hg19-based files can be used for the evaluation.