Enrico Cocchi
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Recent activity by Enrico Cocchi Sort by recent activity-
Hi Pamela Bretscher and Nalini Ganapati, thank you for your suggestion but this is not the issue. GATK Mutect2 automatically creates both a .idx and a .stats file for the generated VCF. I never got...
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Hi Nalini Ganapati. You can see an example VCF here, but I'd like to ask again: this is taking much longer than expected, how can I solve this while you guys investigate the bug? Use a different GA...
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ok, thank you Pamela Bretscher, what can I do to have it working in the meanwhile? Use a different version?
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Hi Pamela Bretscher, here you go: ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
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ok Pamela Bretscher, what error exactly are you talking about? The ValidateVariants output or the GenomicsDBImport empty DB? Looking forward to receive this answer to be able to proceed with my ana...
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Hi Pamela Bretscher, thank you so much for your reply! The VCF files are direct output from Mutect2 command (first command in my original post above), I did not modify them at all. I also tried Val...
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I have a problem with PoN generation Step 2: GenomicsDBImport step creates EMPTY databases from Mutect2 called VCFs: here the link to the Biostar post I created about this. Please comment if you ha...
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Is there any way to get the log2 output instead of the CN from PostprocessGermlineCNVCalls?
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Ok guys I see we are able to download both a gnomAD GENOMES (29 GB) gnomAD EXOMES (2 GB) file from the GATK bundle. And they can be passed directly to CollectAllelicCounts --intervals. I see that...
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How do we download these blacklists that you state you made available?