Isadora Machado Ghilardi
- Total activity 28
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 9
Activity overview
Latest activity by Isadora Machado Ghilardi-
Isadora Machado Ghilardi commented,
Okay! Thank you!Just one more question, to call copy number variants, this is the example code: gatk GermlineCNVCaller \ --run-mode COHORT \ -L scatter-sm/twelve_1of2.interval_list \ -I cvg/HG00096...
-
Isadora Machado Ghilardi commented,
Hi Gokalp I created my scatter using this command: picard IntervalListTools --INPUT cohort.gc.interval_list --SUBDIVISION_MODE interval_count --SCATTER_CONTENT 5000 --OUTPUT scatterIs the same comm...
-
Isadora Machado Ghilardi created a post,
Call copy number variants with GermlineCNVCaller
REQUIRED for all errors and issues: a) GATK version used: 4.3 I`m following this pipeline here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-rare-germline-copy-number...
-
Isadora Machado Ghilardi commented,
Yes, the problem was that the spaces were not separated with a tab. Thank you so much for your help!
-
Isadora Machado Ghilardi created a post,
ValueError in DetermineGermlineContigPloidy
REQUIRED for all errors and issues: a) GATK version used: 4.3b) Exact command used: gatk DetermineGermlineContigPloidy -L cohort.gc.filtered.interval_list --interval-merging-rule OVERLAPPING_ONLY -...
-
Isadora Machado Ghilardi commented,
I'm looking for this document: gs://gatk-sv-resources-public/gcnv-exome/contig_ploidy_prior_hg38.tsv. To use in the setp - DetermineGermlineContigPloidy, but I can't find it.
-
Isadora Machado Ghilardi commented,
Hello!I have a question about the application of CollectVariantcallingmetrics. Should I use in the separeted files generated by the hard filtering (indels and snps)? Should I use in my cohort file?...
-
Isadora Machado Ghilardi commented,
It worked! Thank you!!
-
Isadora Machado Ghilardi commented,
Do I have to do the aggregation step and then do the joint genotype using the GenotypeGVCFs or can I move to the GenotypeGVCFs setp?
-
Isadora Machado Ghilardi commented,
Hello! I`m using the version 4.4.0.0. I did the HaplotypeCaller in my 18 samples, and it worked. Now I`m using the CombineGVCFs to put the samples together in a cohort. However I go this error: Ex...