-
Hi team,
Thanks for sharing this very useful tool. I ran mgatk tenx using my own scATACseq data.
`mgatk tenx -i possorted_bam.bam -n mytest -o mytest_mgatk -c 8 -bt CB -b barcodes.tsv`
I can …
-
MergeGVCFs and ploidy = 1 seems to make the GATK hang.
-
I have 1060 WGS samples and I used MToolBox V1.1 to call MT variants. When looking at the result VCF file, I noticed that my GTs are either 0 or 0/1 with HF, but only 3 variants with 1/1 GTs among abo…
-
Hello,
I am working with human mtDNA. When I assemble it the circularized version starts from the random positions (like 6789, 7345 and so on splitting the mtDNA in the middle) with respect to the …
-
貼吧活動：(請查閱 [SARS-CoV-2 Timeline by 2020.02.21](https://github.com/agorahub/_meta/blob/agoran/theagora/sari/Memorandum_2020-02-21_SARS-CoV-2-Timeline_Nathan.pdf?raw=true), by Nathan :cloud: )
- Colla…
-
Hi,
There is a bug in the new version's output:
"Sample" "Contamination Status" "Overall Homoplasmies" "Overall Heteroplasmies" "Sample Coverage" "Major Haplogroup" "Major Haplogroup Quality" "Min…
gevro updated
5 years ago
-
Hi,
A few issues with the output of the new version.
1) The word "amount" is still used and is unclear what this means.
2) Major Heteroplasmy Level and Minor Heteroplasmy Level are now empty. Thi…
gevro updated
5 years ago
-
Hi, I have a sample for which the Contamination = YES, but the MeanHetLevelMinor = 0. This should not be possible, because by definition, if there is a minor haplogroup, then there should be some leve…
gevro updated
5 years ago
-
Hi. I ran a standard haplocheck analysis and the report said Major Level and Minor Level is 0%, with No contamination.
Here is the contamination.txt file:
"SampleID" "Contamination" "Sampl…
gevro updated
5 years ago