Enrico Cocchi
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Activity overview
Latest activity by Enrico Cocchi-
Enrico Cocchi commented,
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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Enrico Cocchi commented,
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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Enrico Cocchi commented,
ok, thank you Pamela Bretscher, what can I do to have it working in the meanwhile? Use a different version?
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Enrico Cocchi commented,
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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Enrico Cocchi commented,
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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Enrico Cocchi commented,
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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Enrico Cocchi created a post,
Mutect2 PoN - GenomicsDBImport creates empty DB
AnsweredI am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \-R ${REF} \-L ${EXOME_INPUT_INTERVALS} \-I ${...
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Enrico Cocchi commented,
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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Enrico Cocchi commented,
Is there any way to get the log2 output instead of the CN from PostprocessGermlineCNVCalls?
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Enrico Cocchi commented,
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...