Tag: HTSlib

query regarding error in installation of “goseq” R bioconductor package

query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…

Continue Reading query regarding error in installation of “goseq” R bioconductor package

How can I visualize the output of BAM metrics files generated by samtools stats?

How can I visualize the output of BAM metrics files generated by samtools stats? 1 I have a few dozen BAM files and I used samtools stats to generate .txt files containing the outputted BAM metrics for each of my BAMs. I would now like to visualize this output to…

Continue Reading How can I visualize the output of BAM metrics files generated by samtools stats?

Are package downgrades a necessary evil in Conda?

Are package downgrades a necessary evil in Conda? 1 I am just trying to get my head around using conda environments. I created a conda environment for a project containing plink2, plink, R and bcftools. When I installed plink, using mamba install -n autozygosity -c conda-forge plink, I got the…

Continue Reading Are package downgrades a necessary evil in Conda?

Index of /~psgendb/doc/pkg/samtools-1.7/htslib-1.7/cram

Name Last modified Size Description Parent Directory   –   cram.h 2015-06-24 11:00 2.4K   cram_codecs.c 2017-09-26 09:28 50K   cram_codecs.h 2016-03-17 07:48 6.0K   cram_codecs.o 2018-03-04 16:57 175K   cram_decode.c 2018-01-26 05:33 84K   cram_decode.h 2013-10-16 06:15 3.4K   cram_decode.o 2018-03-04 16:57 236K   cram_encode.c 2017-07-03 16:45 87K  …

Continue Reading Index of /~psgendb/doc/pkg/samtools-1.7/htslib-1.7/cram

Index of /~psgendb/birchhomedir/public_html/doc/pkg/samtools-1.7/htslib-1.7/htslib

Name Last modified Size Description Parent Directory   –   bgzf.h 2018-01-10 07:45 14K   cram.h 2015-09-25 05:36 15K   faidx.h 2017-02-07 11:06 5.6K   hfile.h 2018-01-26 05:33 9.6K   hts.h 2017-11-24 09:46 29K   hts_defs.h 2017-08-10 11:07 3.3K   hts_endian.h 2017-09-27 10:40 11K   hts_log.h 2017-06-03 15:45 3.8K  …

Continue Reading Index of /~psgendb/birchhomedir/public_html/doc/pkg/samtools-1.7/htslib-1.7/htslib

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…

Continue Reading How To Install libhts-dev on Kali Linux

Samtools Htslib Issues

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

Continue Reading Samtools Htslib Issues

Ubuntu Manpage: samtools targetcut – cut fosmid regions (for fosmid pool only)

Provided by: samtools_1.13-2_amd64 NAME samtools targetcut – cut fosmid regions (for fosmid pool only) SYNOPSIS samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] in.bam DESCRIPTION This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and…

Continue Reading Ubuntu Manpage: samtools targetcut – cut fosmid regions (for fosmid pool only)

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…

Continue Reading Detailed differences between sambamba and samtools

bam – samtools view command not found error

When I tried to use samtools to split a bam file based on different chromosomes, I used this command: samtools view input.bam -b chr21 | chr21.bam However, I get error messages like this: -bash: chr21.bam: command not found [W::hts_idx_load3] The index file is older than the data file: input.bam.bai How…

Continue Reading bam – samtools view command not found error

JUWELSBOOSTER module browser

HTSlib Compiler/GCCcore/11.2.0 1.14 Description =========== A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix More information ================ – Homepage: www.htslib.org/ – Site contact: Support <sc@fz-juelich.de>, software installed by Alexandre Strube <a.strube@fz-juelich.de> EBROOTHTSLIB /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0 EBVERSIONHTSLIB 1.14 EBDEVELHTSLIB /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/easybuild/Compiler-GCCcore-11.2.0-HTSlib-1.14-easybuild-devel +CMAKE_PREFIX_PATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0 +CPATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/include +LD_LIBRARY_PATH /p/software/juwelsbooster/stages/2022/software/HTSlib/1.14-GCCcore-11.2.0/lib…

Continue Reading JUWELSBOOSTER module browser

sam – Use Htslib to create auxilary tags in bam file C++

I am creating a threaded c++ file where i generate in silico bam files, using header, DNA sequence and read information. First i use bam_init1() to create the bam1_t structure just named “b”. Then i use bam_set1 to create the actual sequence entry in the bam file bam_set1(b,read_id_length,READ_ID,flag,chr_idx,min_beg,mapq,n_cigar,cigar,-1,-1,0,strlen(DNAsequence),DNAsequence,quality_string,l_aux) And finally…

Continue Reading sam – Use Htslib to create auxilary tags in bam file C++

bioconductor – Trouble installing Rhtslib in R/R studio

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

Continue Reading bioconductor – Trouble installing Rhtslib in R/R studio

Ubuntu Manpage: samtools reheader – replaces the header in the input file

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

Continue Reading Ubuntu Manpage: samtools reheader – replaces the header in the input file

Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

Continue Reading Fail to install Ensembl VEP

Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant – C samtools

Thanks for getting back to me Valeriu. As you suggested, I used the latest commit from the develop branch in my pipeline, and the results look good. I was able to replicate the numbers from samtools v1.10.2 and v1.11 for both variant callers. FYI $ docker run scilifelabram/htslib:dev_proper /opt/samtools/samtools version…

Continue Reading Running samtools view on bam affects the number of variants called by both haplotypecaller and deepvariant – C samtools

Access read group tag for BAM reads – rust-htslib

I’m sure this is probably straightforward, but I can’t figure out how to access the read group information on a per-read basis within a BAM file. I can get it from the header, but I can’t determine how to use aux or any other record method to get that info….

Continue Reading Access read group tag for BAM reads – rust-htslib

kojix2/ruby-htslib: v0.0.4 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5797825 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg)](https://doi.org/10.5281/zenodo.5797825) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg :target: doi.org/10.5281/zenodo.5797825 HTML <a href=”https://doi.org/10.5281/zenodo.5797825″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg Target URL doi.org/10.5281/zenodo.5797825 Read more here: Source link

Continue Reading kojix2/ruby-htslib: v0.0.4 | Zenodo

Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

Continue Reading Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

Continue Reading Issues installing Pindel from git

cellranger count DETECT_COUNT_CHEMISTRY (failed)

cellranger count DETECT_COUNT_CHEMISTRY (failed) 0 I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command. cellranger-6.1.1/cellranger count –id pbmc_1k_v2_example –transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A –fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs I get following message. Martian Runtime…

Continue Reading cellranger count DETECT_COUNT_CHEMISTRY (failed)

plotting roh from bcftools

plotting roh from bcftools 0 Heys, I am following this small tutorial on how to calculate ROHs from a vcf file using bcftools (samtools.github.io/bcftools/howtos/roh-calling.html) and I am getting this txt file: # This file was produced by: bcftools roh(1.10.2+htslib-1.10.2-3) # The command line was: bcftools roh -G30 –AF-dflt 0.4 my_file.vcf…

Continue Reading plotting roh from bcftools

User friendly (visual&interactive) VCF/BCF mining tools (2021)

What is currently the best user friendly (visual and interactive) VCF/BCF mining tool in 2021? For VCF/BCF similar to size or even larger than the 1000 human genomes VCF? I guess most organization do not have a visual and interactive mining VCF mining tool but use either: A website front-end…

Continue Reading User friendly (visual&interactive) VCF/BCF mining tools (2021)

tabix for ID column

tabix for ID column 4 Hello, I’m looking for something similar to tabix. But instead of looking for informations within a given region, I would like to use the values in the ID column for quickly lookup. So for example I would like to take the compressed dbSNP file, index…

Continue Reading tabix for ID column

install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

Continue Reading install GenomicFeatures fail

bcftools merge; retaining sample names

bcftools merge; retaining sample names 2 When I do bcftools merge, the headers do not retain the filenames.  How can I specify filenames? This is my command  bcftools merge vcf/unfiltered/*.vcf.gz -O z > msa/pooled.vcf.gz However this is the relevant part of my header, despite the filenames I gave it.  Is…

Continue Reading bcftools merge; retaining sample names

Disappearing CB, the bam tag after samtools sort -t CB

  I’ve been trying to setup an analysis pipline for RNAvelocity in AWS EC2. I used one of the 10x dataset, 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed, as a test model to setup the pipeline. For speed and cost saving, I first used samtools…

Continue Reading Disappearing CB, the bam tag after samtools sort -t CB

What does samtools mean by ‘orientation’ when marking duplicates?

What does samtools mean by ‘orientation’ when marking duplicates? 0 Hello Biostars, It is my understanding that samtools marks duplicates on the basis of the 5′ position of reads and also the orientation of reads. This is based on my reading of the following: www.htslib.org/algorithms/duplicate.html However, I am not sure…

Continue Reading What does samtools mean by ‘orientation’ when marking duplicates?