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…
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 •…
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…
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…
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 …
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…
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…
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…
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…