Tag: sambamba
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…
pjotrp/sambamba – sambamba – Genenetwork
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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…
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…
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…
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…
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…
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…