Tag: sambamba

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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