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Hello ichorCNA team! I'd like to know if your softwar can also be used to analyze shallow whole genome sequencing data comming from tumor tissue samples (not cfDNA but solid samples of the actual tumo…
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Hi,
Are there reference files available to perform imputation on CHM13-v1 aligned data?
Also, would QUILT work on high-cvg (~35x) whole genome sequencing, to help find the very small number of mis…
gevro updated
2 years ago
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Hi, I'm a new to cnvkit. Thanks for this excellent tool. As it was pointed out in the documentation, CNVkit is primarily designed for use on hybrid capture sequencing data, where off-target reads are …
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This command consumed about 60G RAM. But it phased only 10Mb area. I still left about 2500Mb area to phase. how can I reduce the RAM when phasing a large cohort (~1200) of whole-genome sequencing data…
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### Name of the tool
`picard CollectWgsMetricsWithNonZeroCoverage`
### Tool homepage
https://github.com/broadinstitute/picard
### Tool description
Collect metrics about coverage and performance o…
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The journal article uses purified cancer cells (and does not state what flow cytometry markers were used for sorting by).
> ... with sample-matched, flow-sorted WGS.
The software user manual men…
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Hi. I've been using your software to perform a pedigree study of whole genome sequencing data.I drew histograms of AB and GQ using Slivar DDC, and next I had a problem selecting thresholds based on th…
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https://doi.org/10.1101/092890
> Next-generation sequencing (NGS) is a rapidly evolving set of technologies that can be used to determine the sequence of an individual's genome by calling genetic v…
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Hi. Let me describe my data to see if I can use XYalign to find Y-contigs
My data is whole genome re-sequencing data with coverage of ~ 15X, including male and female fish (around 20 each sex)
I h…
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We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
5 months ago