Enrico Cocchi
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Activity overview
Latest activity by Enrico Cocchi-
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...
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Enrico Cocchi created a post,
GATK Mutect2 tumor vs. normal sample
a) How do I compared somatic variants called through a PoN file with the latest best-practive-guidelines between a normal-sample and a tumor-sample in order to know which one are characteristics of...
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Enrico Cocchi commented,
How do we download these blacklists that you state you made available?
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Enrico Cocchi commented,
Hi, can you please explain what's exactly the role of -tumor-segmentation segments.table in CalculateContamination and how we're supposed to generate such table?
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Enrico Cocchi commented,
Panel-of-Normals file generation, GenomicsDBImport file merge, I got the following error message several times: [E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64...
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Enrico Cocchi commented,
Hi Nickier, I had the same problem and figured out it's basically related to how contigs are passed from the BED file. If the BED (or interval_list as they call it) has a lot of different little in...
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Enrico Cocchi commented,
Hi, I am trying to use your pipeline in gatk 4.1.7 but I saw that the output of passage 2 (GenomicsDBImport) is a folder with some files in it, such as vcfheader.vcf, vidmap.json and what looks lik...
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Enrico Cocchi commented,
I'll try it tomorrow, but do you guys know why is this happening?
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Enrico Cocchi created a post,
Mutect2 missing variant
Hi, I am using GATK 4.1.2.0 and I noticed a strange behavior by Mutect2. The variant 13-33329989-TGTCTC-T is called if the BED file contains: 13 33329959 33330170 but not if it contains: 13 3...