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Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data

rare variant umi resequencing ctdna tool written 21 months ago by mikhail.shugay ♦ 3.3k • updated 25 days ago by alons • 270

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Any good SV calling software for CtDNA?

sv software ctdna written 18 months ago by wang.vic • 0 • updated 18 months ago by d-cameron • 2.0k

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Problems using cnvkit for ctDNA targeted sequencing

cnvkit ctdna results written 18 months ago by ingrid.schulman • 0 • updated 18 months ago by Eric T. • 2.3k

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Job: Senior Bioinformatician Position at AnchorDx

ctdna next-gen methylation job somatic mutation written 22 months ago by weihong_xu • 30

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Detecting variants at very low fractions from ctDNA

ctdna mutation variants written 2.3 years ago by CY • 270 • updated 2.3 years ago by Tonor • 420

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Recent Replies

C: Filter Fastq file by seq by ta_awwad • 200
this is awesome .. thank you so much
C: Filter Fastq file by seq by finswimmer ♦ 10k
You could use `repair.sh` from [BBtools][1] to remove the corresponding paired read after removi...
C: GBS paired reads splits it into several smaller files based on barcode matching by cpad0112 ♦ 11k
did you try GBSX tool? https://www.biostars.org/u/36776/
C: Data managment (Hadoop/Spark) and sequencing data by Devon Ryan ♦ 88k
The thing with using Hadoop/Spark is that few bioinformatics tools support them. So you can use s...
C: DESeq2 for two file.BAM by cpad0112 ♦ 11k
as https://www.biostars.org/u/25721/ says results will not be statistically meaningful and unrel...
C: Paired end peak callers by Dataminer • 2.6k
Hi Fredrieke, Thank's for the Genrich. I am not after any specific functionality, in general I h...
C: How to check the presence of mutations of a specific gene in a specific VCF file by finswimmer ♦ 10k
Yes and yes :) The important thing to understand is, that a `vcf` doesn't know anything about ge...
C: Genomics (DNA) Pipeline - Example by finswimmer ♦ 10k
If you start snakemake with the `--cores` parameter e.g. `--cores 4` it runs 4 jobs in parallel. ...
C: Filter Fastq file by seq by ta_awwad • 200
thank you so much .. is there any option to remove the read of the same fragment from both paired...
C: how to remove pig sequences from metagenomics data by Carambakaracho • 790
> I could not find a pig genome database seriously? here's a second one just three keystrokes...
C: Some problems using rMATs by tomoya • 0
Even I have successfully installed gcc5, gel and numpy, I still get the same error. This time I u...
C: problem in conversion of sam to bam file by ATpoint ♦ 13k
Agreed. As I told you already, your SAM file is corrputed because STDERR messages are in it. Star...

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