Tag: sambamba

Hello, I know Brian is sometimes around, but here is my command: while read p; do callvariants.sh in=${p}.recal.bam ploidy=2 vcf=${p}.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g ; done <ID java -ea -Xmx50g -Xms50g -cp /home/alessandro/software/bbmap/current/ var2.CallVariants in=ancestor.recal.bam ploidy=2 vcf=ancestor.20score.vcf useidentity=f overwrite=true ref=ref.fsa -Xmx50g Executing var2.CallVariants [in=ancestor.recal.bam, ploidy=2, vcf=ancestor.20score.vcf, useiden tity=f, overwrite=true, ref=Adineta_vaga.fsa,…

Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…

Tong, S. & Revill, P. Overview of hepatitis B viral replication and genetic variability. J. Hepatol. 64(1 Suppl), S4–S16 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Kramvis, A. Genotypes and genetic variability of hepatitis B virus. Intervirol. 57(3–4), 141–150 (2014). Article  Google Scholar  Cao, L. et al. Coexistence of…

What is the correct procedure to generate a consensus bacterial sequence? 0 Hello, I would like to create a consensus sequence of a bacterium starting from the fastq files generated with Illumina. I proceeded as follows: 1. Remove poor quality sequences with trimmomatic (SLIDINGWINDOW:4:30) 2. Align with BWA MEM2 (piped…

How to generate a consensus sequence from BAM file with bcftools? 0 Hello, I have aligned some files against a reference genome with BMA-MEM, deduplicated and sorted with sambamba to generate a AlnSrtDedSrt.bam file. The question is: how can I generate a consensus fasta file? I have this fragment of…

Luo T, Comas I, Luo D, et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci USA. 2015;112:8136–41. Article  CAS  PubMed  PubMed Central  Google Scholar  Yin QQ, Liu HC, Jiao WW, et al. Evolutionary history and ongoing transmission of phylogenetic…

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? 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 •…

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? 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…

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 …

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 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…

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…

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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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 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 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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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 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…