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Every overlapping read pair in HaplotypeCaller and Mutect2
goes through `FragmentUtils.adjustQualsOfOverlappingPairedFragments`, which has the following *hard-coded* logic:
```
if ( firstReadBa…
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That is, multiple samples of the same tumor in space or time, a tumor and a metastasis, a tumor and its cfDNA etc.
First we have to ask collaborators and the community what features they would like…
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Hi, I have read paper of SViCT and tried to use this tool for my analysis
The compilation was successful and ran this tool using cfDNA sample and the core dump has raised.
Command line I have us…
tahuh updated
5 years ago
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Hi Dinh,
I would like to ask you a question.I have bisulfite sequencing data from cfDNA captrued with target probe.Therefore,for a specific region,the haplotypes may have different start and end as…
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Hi,
I have been trying to call variants on liquid biopsy samples using the variantCaller (TVC) 5.10.0.18 -and then with 5.10.0.20 from within Ion Torrent Suite (ITS) server web interface applicatio…
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I've some maternal blood cfDNA (containing both maternal and fetal DNAs) sequenced bam files. Whether this method can be used for predicting fetal sex?
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I'm seeing error messages relating to certain reads that seem unremarkable except that they contain N's. Like this:
```
Z/r/job6pcRlf [2017-07-05T15:44:45.538328] [blade15-1-16.gsc.wustl.edu] …
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My samples have rather low purity, because these are gastric cancer tumors and it is typical for the tumor to be diffuse. Consequently, PureCN makes a lot of calls of purity = 0.15, and many of my sa…
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This is most probably an issue upstream with the data submission.
Example:
https://www.targetvalidation.org/evidence/ENSG00000133703/EFO_0000096
Title of the abstract: Circulating tumour DNA seque…
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Hi Felix,
Another question for you -- I'm looking at M-bias for my samples (8-10x WGBS) and I'm noticing that there is definitely a dropoff of methylation at the start of the read, but it goes back…
caalo updated
6 years ago