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## Case study
* Agency / office: Veterans Administration
* Contact: Gil Alterovitz (gil.alterovitz@pif.gov)
* Type of data:
Electronic medical record data, administrative and demographic inform…
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I applied MTAG https://github.com/omeed-maghzian/mtag for some public data:http://csg.sph.umich.edu//abecasis/public/lipids2013/. I choose Total Cholesterol and Triglycerides data to test MTAG.
Whe…
umcyh updated
6 years ago
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Hello,
Just hoping to get some insight into these smudgeplots that I have generated based on Illumina HiSeq data. These are for two closely related tree species. I've also attached the genomescop…
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Hello!
thanks for your amazing tool. I was trying to run PAPipe with my own data, but the analysis kept crushing at the variant calling step. When I was trying to figure out what was the problem, …
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Hi,
Thanks for this very cool tool!
Could you please suggest a way to determine sex of every sample in vcfR?
One approach I know is heterozygosity rate on chrX. However, not sure how to calclaut…
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Please provide links to the raw data and the scripts necessary to format them for JBrowse. I would like to set up my own instance using data of known provenance and a proven chain of custody. Pullin…
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### Affected version(s)
- [x] MUTECT 2.2
### Description
Using GATK Mutect2, we collected several variants in EGFR region.
However, one variants NM_005228.5(EGFR):c.2239_2248delinsC (p.Le…
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Hi @J35P312
I am trying to identify SV (translocations mainly) in patients with know translocations. I am setting up the pipeline with a patient with t(14:18) and I have a single-cell bam file (2000…
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Would it be possible to perform the matrix processing stage on a per-chromosome basis to allow distribution of the work?
Thanks!
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# Scratch pad
hs38 primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV
hs38a hs38 plus ALT contigs
hs38DH hs38a plus decoy contigs and HLA genes (r…