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Any good SV calling software for CtDNA?

sv software ctdna written 8 months ago by wang.vic • 0 • updated 8 months ago by d-cameron • 1.5k

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484

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Problems using cnvkit for ctDNA targeted sequencing

cnvkit ctdna results written 8 months ago by ingrid.schulman • 0 • updated 8 months ago by Eric T. • 2.1k

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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 11 months ago by mikhail.shugay ♦ 3.2k

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645

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Job: Senior Bioinformatician Position at AnchorDx

ctdna next-gen methylation job somatic mutation written 12 months ago by weihong_xu • 30

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Detecting variants at very low fractions from ctDNA

ctdna mutation variants written 17 months ago by CY • 100 • updated 17 months ago by Tonor • 420

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Recent Replies

A: Matching peptides which differ by one letter? by cpad0112 • 4.4k
in R: df1= read.csv("test1.txt", sep = "\t", stringsAsFactors = F, header = F) df2= read...
C: Recalibration step from SNP calling by mostafarafiepour • 0
Excuse me, is the Recalibration stage really necessary or can it be ignored?
C: Are there any GNU parallel or similar Shell/Bash code examples on how to run Sna by ole.tange • 3.0k
Or shorter: `ls *_1.fastq.gz | parallel --plus "bwa mem idx.fa {} {%_1.fastq.gz}_2.fastq.gz > ...
C: Recalibration step from SNP calling by mostafarafiepour • 0
an empty VCF file ? Sorry, I do not understand what you mean ?
C: Recalibration step from SNP calling by Pierre Lindenbaum ♦ 106k
then try to provide an empty VCF file as the database....
C: Recalibration step from SNP calling by mostafarafiepour • 0
many thanks for your reply, yes i didn't provide "A database of known polymorphic sites to mask...
A: How to extract from a fasta file, all the protein sequences that have more than by cpad0112 • 4.4k
For future reference, to filter a multifasta file for sequences with more than 800 aa, $ se...
A: Recalibration step from SNP calling by Pierre Lindenbaum ♦ 106k
https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_too...
C: Needleman Wunsch algorithm coding in python for global alignment by finswimmer • 1.4k
Hello hbleed121, what kind of trouble are your facing? Please be more specific. Or is it just a ...
C: Matching peptides which differ by one letter? by Alex Reynolds ♦ 23k
That bit at the end is pretty darn clever. Wish I could give more than one vote, but I'm not Putin.
A: Get sequences for KEGG by EC and taxa by natasha.sernova • 2.9k
These posts may be helpful: https://www.biostars.org/p/71737/ https://www.biostars.org/p/55962/...
C: Display full information about taxa instead of staxids in BLASTn by h.mon ♦ 13k
staxid means Subject Taxonomy ID staxids means unique Subject Taxonomy ID(s), sepa...

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