Tag: sambamba

Why is coordinate sort required before findng read depths?

Why is coordinate sort required before findng read depths? 1 I have a wgs dataset and when I attempt use it with sambamba depth command, it gives sambamba-depth: All files must be coordinate-sorted error. What is the reason for this and why coordinate sorting is required? wgs sambamba • 28…

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Why coordinate sort is required in sambamba depths?

Why coordinate sort is required in sambamba depths? 0 When I run the command sambamba depth base -L genomicdataset001.bed $filename It gives the following error sambamba-depth: All files must be coordinate-sorted Why coordinate-sort is required in this run and what coordinate sorting is exactly? sorting coordinate sambamba linux samtools •…

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All files must be coordinate-sorted error?

sambamba-depth: All files must be coordinate-sorted error? 1 I am trying to use sambamba to an indexed whole genome dataset. basename_X $dataset f=”$(basename_X — $dataset)” sambamba depth base -L genomic.bed $dataset> ./reads/”$f.txt” However, the above script gives the following error. sambamba-depth: All files must be coordinate-sorted What is the reason…

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Samtools index and sambamba-depth error?

Samtools index and sambamba-depth error? 0 I have the following script samtools index dataset01.bam basename dataset01.bam f=”$(basename — dataset01.bam)” sambamba depth base -L genomic.bed dataset01.bam > ./read_depths/”$f.txt” I run this script with a whole genome dataset and after that is gives the following error. samtools index: failed to create or…

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Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

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Best Practices for CRAM BAM

Forum:Best Practices for CRAM <-> BAM 0 Hi, I am looking for advice about transitioning from bam/bai to cram for archival purposes. General advice is appreciated, but I’m specifically looking for answers to these two questions – Does samtools offer the best performance for converting to and from CRAMs? Do…

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samtools idxstats not removing ChrM

samtools idxstats not removing ChrM 2 I am trying to remove ChrM from my ChIP-seq data. Below is my pipeline for one sample up to where I am having the issue (samtools idxstats). The output file from samtools idxstats is the same size as the input so it doesn’t look…

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How To Install libhts-dev on Kali Linux

In this tutorial we learn how to install libhts-dev on Kali Linux. libhts-dev is development files for the HTSlib Introduction In this tutorial we learn how to install libhts-dev on Kali Linux. What is libhts-dev HTSlib is an implementation of a unified C library for accessing common file formats, such…

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Detailed differences between sambamba and samtools

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

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pjotrp/sambamba – sambamba – Genenetwork

10 years ago ​ 10 years ago ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10 years ago ​ ​ ​ ​ ​ ​ 10 years ago 10 years ago 10 years ago ​ ​ 10 years ago ​ 10 years…

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Ubuntu Manpage: sambamba-view – tool for extracting information from SAM/BAM files

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

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How to call LOH with FreeC

How to call LOH with FreeC 0 Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the “[BAF]” section of the configuration file: [BAF] makePileup = My_somaticVCF.vcf.gz fastaFile = hg19.fa SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz When…

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Strange speed up in GATK LeftAlignIndels

Strange speed up in GATK LeftAlignIndels 1 Hi! I noticed a strange thing, I have been running a DNA-seq pipeline like this: reads -> bwa-mem2 -> picard SortSam -> picard MergeSamFiles -> picard MarkDuplicates -> gatk LeftAlignIndels … gatk LeftAlignIndels has always taken around 4 hours to complete with the…

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nanopore sequencing stock

It holds a 15% stake in the company and has valued its holding at £340m, giving a valuation of more than £2bn for the company. . While the company’s current shareholders have recorded its value at just over £2bn, analysts . Essay from the year 2011 in the subject Business…

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Sambamba markdup usage help

Sambamba markdup usage help 0 Hi! I need so help regarding the usage of sambamba markdup. I have read the documentation but I don’t quite understand. What is meant by insert size here? –hash-table-size=HASH_TABLE_SIZE size of hash table for finding read pairs (default is 262144 reads); will be rounded down…

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Sambamba

Sambamba 1 Hi can anyone guide me how to install sambamba package in ubuntu 20.04 install sambamba ubuntu • 22 views The documentation for getting binary (64bit linux) packages and compiling this software from source is found on the home page of the package: lomereiter.github.io/sambamba/ If you need more help…

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