Tag: HTSlib

I have used kallisto in the past, but now am struggling to get bootstrapping to work on a new computer (MacBook M1). I have searched through the issues that others encountered and tried three different methods of installation, but still no luck. Could you please help or direct me to…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 18 Nov 2023 16:34:59 +0100 Source: bedtools Architecture: source Version: 2.31.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1055414 Changes: bedtools (2.31.0+dfsg-2) unstable; urgency=medium . * gcc-13.patch: fixed upstream by different change….

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 07 Nov 2023 19:46:30 +0100 Source: htslib Architecture: source Version: 1.18+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: htslib (1.18+ds-1) unstable; urgency=medium . * Migrate htslib 1.18 from experimental to unstable. Checksums-Sha1:…

Abstract Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5–8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new…

I am trying to convert my vcf file into a BED format file.  When I use this command: plink –vcf merge.bacteria.vcf.gz –make-bed –out merge.bacteria.vcf.bed  I get the following error stating:  PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License…

Tutorial:NGS one-liner to call variants 0 This is a tutorial about creating a pipeline for sequence analysis in a single line. It is made for capture/amplicon short read sequencing in mind for human DNA and tested with reference exome sequencing data described here. I share the process and debuging steps…

Hi, I ran kallisto and got 2 files as output: abundance.tsv and run_info.json. I do not get an abundance.h5 file, as stated in the manual. I have 2 questions: 1. Is there a way to use sleuth without relying on HDF5 files? 2. I followed all the instructions for downloading the…

Tutorial:NGS oneliner 0 This is a tutorial about creating a pipeline for sequence analysis in a single line.I share the process and debuging steps gone through while putting it together.Source is available at: github.com/barslmn/ngsoneliner/I couldn’t make a longer post, complete version of this post: omics.sbs/blog/NGSoneliner/NGSoneliner.html Pipeline # fastp –in1 “$R1″…

Hello, this question is somehow complementary to what I asked yesterday here: Using bcftools to find unique alt homozygous sites Now let’s say I want to find the SNPs 0/1 unique to the sample D3A350g_bcftools2 (see below) I know I can use bcftools view -s D3A350g_bcftools2.bcf -x all_bcftools2_merged.vcf But there…

I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I’m facing the problem that I seem to be unable to use it in PLINK or find the correct data format to download at all, and I am a bit…

Hello, I have a vcf with 20 samples. I want to find for each sample the sites that are 1/1, only in that sample (so other samples must have genotypes 0/1 or 0/0). I know I can use filters such as GT=”aa”‘ However, how do I say GT=”aa” for sample…

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

Hi all, i am trying to merge two VCF files using bcftools merge. However, my command bcftools merge -m id VCF_d.vcf.gz VCF_p.vcf.gz -o merged.vcf.gz –force-samples returns the following The REF prefixes differ: TG vs GA (2,2) Failed to merge alleles at 18:786377 in VCF_d.vcf.gz These are the entries in the…

Provided by: samtools_1.10-3_amd64 NAME samtools phase – call and phase heterozygous SNPS SYNOPSIS samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam DESCRIPTION Call and phase heterozygous SNPs. OPTIONS -A Drop reads with ambiguous phase. -b STR Prefix of BAM output. When this option is in use,…

Cargo Features [dependencies] rust-htslib = { version = “0.44.1”, default-features = false, features = [“bindgen”, “bzip2”, “curl”, “gcs”, “libdeflate”, “lzma”, “s3”, “serde_feature”, “static”] } default = bzip2, curl, lzma These default features are set whenever rust-htslib is added without default-features = false somewhere in the dependency tree. bindgen Enables bindgen…

Hi, I am trying to run CONTROL-FREEC on diploid yeast samples to detect CNVs on a department cluster. The config file looks like this: [general] chrLenFile = yeast_chr.len ploidy = 2 window = 150000 #breakPointThreshold = -.002; #coefficientOfVariation = 0.062 chrFiles = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/yeast_files outputDir = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/output #degree=3 [sample] mateFile =…

How to change the output reference for vg giraffe BAM output 1 I constructed a pan genome graph with mingraph cactus with two reference genomes specified. I am trying to align reads to the graph and produce a BAM file that is specific to one of the references. How can…

This is just a tiny tutorial on how to build mosdepth on Mac. There is currently no version for Mac available at conda (hope that changes soon, edit (3/2021): it did change, see anaconda.org/bioconda/mosdepth), and from what I’ve read building from source was a pain so far, still these simple…

I have a BAM file and its index on a web host: $ ll HUDEP.control.DS182418.chr22.bam* -rw-r–r– 1 areynolds stamlab 14046407041 Jul 31 21:57 HUDEP.control.DS182418.chr22.bam -rw-r–r– 1 areynolds stamlab 1340656 Jul 31 21:57 HUDEP.control.DS182418.chr22.bam.bai As a positive control, I can query this file via the HTTPS protocol from a web application…

how to change the ‘bcftools plugin’ temp directory 0 Hi, \ I am using the bcftools plugin ‘liftover’, cat input.vcf | bcftools +liftover –threads 10 -Oz -o output.liftover.vcf.gz — -s original_reference.fna -f new_reference.fna -c original_to_new.chain 2>liftover.log but my runs fail with the following error: [main_plugin] Error: cannot write to Perognathus_filtered.liftover.vcf.gz…

Efficient Way to Split Huge VCF Files by Chromosome | Inquiry 1 Hello, I have been spending significant time trying to split a large VCF file into its individual chromosome files. Here is the code I have been using (it works, but in a very inefficeint manner): for i in…

Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: j…@freebsd.org Log URL: pkg-status.freebsd.org/ampere1/data/131releng-armv7-quarterly/bee14067723b/logs/htslib-1.17.log Build URL: pkg-status.freebsd.org/ampere1/build.html?mastername=131releng-armv7-quarterly&build=bee14067723b Log: =>> Building biology/htslib build started at Mon Jul 10…

RNAseq comparing wt strain PcPCL1606 and the derivative mutant AdarB, defective in HPR production. RNA was extracted from the rhizosphere samples using a PowerSoil® RNA extraction kit (Qiagen Iberia S.L., Madrid, Spain) following the manufacturer’s instructions and its amount was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham,…

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files. To clone this repository, issue $ git clone –recursive github.com/rust-bio/rust-htslib.git ensuring that the HTSlib submodule is fetched, too. If you only want to use the library, there is no need to clone the…

HTSlib threads when ingesting large bgzipped FASTA 0 Is it possible to use HTSlib thread pool when loading large (genomic) FASTA sequences? Here’s a sample code: #include <htslib/hts.h> #include <htslib/sam.h> #include <htslib/faidx.h> #include <htslib/bgzf.h> #include <htslib/thread_pool.h> char fn[] = “/path/to/bgzipped.fasta.fa.gz”; int nthreads = 4; faidx_t *faidx = fai_load(fn); hts_tpool *tpool…

Samtools sort error: [pretty_header] invalid header 1 Hello, I want to convert my .sam files into .bam files with Samtools. Samtools view functioned well, here’s my code: (My sam files have the @ indicator, indicating the header. If I use head on my files: @SQ SN:NC_000067.7 LN:195154279 @SQ SN:NT_166280.1 LN:169725…

I am trying to activate a conda environment from snakemake to use a different environment for a rule in the workflow. I created a .yml file to specify dependencies. This is the snakemake rule I defined: rule Merge_VCFs: input: f1=’file1′ f2=’file2′ output: vcf=”output_file” conda: “bcftools_env.yml” shell: “”” bcftools merge -m…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 22 Jun 2023 22:21:42 +0200 Source: htslib Architecture: source Version: 1.17+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Changes: htslib (1.17+ds-1) unstable; urgency=medium . * Migrate htslib to unstable. * d/control: declare libhts3…

rust_htslib unrecognized filter ID 1 Hello, I am just starting Rust and I wanted to use rust_htslib to process a VCF. Idea was to set a filter flag (here AFnfe) in all records having AF>0.1. Yet I have troubles adding this filter: code compiles but fails because the id AFnfe…

Source: samtools Version: 1.16.1-1 Severity: important Tags: ftbfs Hi, When samtools is tested against htslib 1.17 now available in experimental, I witness the following error, either from build time checks or from autopkgtest: The command failed [256]: /tmp/autopkgtest.PsRbbX/autopkgtest_tmp/samtools view -e ‘pos<1000||pos>1200’ -O cram,embed_ref=1 -T test/dat/mpileup.ref.fa -o /tmp/autopkgtest.PsRbbX/autopkgtest_tmp/test/reference/mpileup.1.tmp.cram test/dat/mpileup.1.sam out: err:[E::validate_md5]…

What’s the correct way to store bam record in a vector and free them? 1 Here’s my demo code #include <stdio.h> #include “htslib/sam.h” #include <vector> #include <fstream> #include <string> #include <iostream> int main(int argc, char *argv[]) { samFile *fp = sam_open(argv[1], “r”); hts_idx_t *idx = sam_index_load(fp, argv[1]); bam_hdr_t *h =…

I would like to read iteratively the same BAM file twice using htslib. My option is to use hts_open, sam_hdr_read, then sam_read1 as much as needed to read the file until EOF. Is there a possibility to “rewind”, and use sam_read1 again from the beginning of the file, without closing…

htslib-1.15.1-2.fc38 – Fedora Packages ↵ Return to the main page of htslibView buildSearch for updates Package Info (Data from x86_64 build) Changelog Dependencies Provides Files Changelog Date Author Change 2023-01-19 Fedora Release Engineering <releng at fedoraproject dot org> – 1.15.1-2 – Rebuilt for fedoraproject.org/wiki/Fedora_38_Mass_Rebuild 2022-08-15 John Marshall <jmarshall at hey…

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Tried to create an environment using Conda and was not able to do so. Have copy pasted the message below. Would be grateful to know what the issue is and how to resolve the issue. (base) C:\Users\Mathangi Janakiraman>wget data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml–2023-05-11 12:54:47– data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.ymlResolving data.qiime2.org (data.qiime2.org)… 54.200.1.12Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443… connected.ERROR: cannot verify…

I am trying to run a snakemake pipeline with packages installed from a main.yml file. One of the dependencies of the package is samtools, Previously, having the dependency listed as samtools did not seem to run into any problems. The actual yml file is: name: yevo_pipeline_env channels: – defaults -…

Issue With CRAM -> BAM -> FASTQ Conversion 2 Please help! I am trying to obtain fastq files from the GDSC, all we have in the lab is CRAM files. Unfortunately, the reference genome seems to not exist when pulled from an online source. I have attempted to use the…

doing PBS(population branch statistics) in ANGSD 0 Hi everyone, i am trying to do a Population branch statistic on my data i have done the first step where i calculate saf, now i need to do the second step calculating 2dsfs. when i submit the script on the cluster. I…

Provided by: samtools_1.16.1-1_amd64 NAME samtools-phase – call and phase heterozygous SNPs SYNOPSIS samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam DESCRIPTION Call and phase heterozygous SNPs. OPTIONS -A Drop reads with ambiguous phase. -b STR Prefix of BAM output. When this option is in use, phase-0…

MethylR on bam files Gives Error 0 I used bismark to get bam files and now trying to implement processBismarkAln() on it but getting the following error: Using htslib. Error: Unexpected cigar: M As far as I know, some possible causes of this error could include: 1)A problem with the…

Filter out Bam not overlapping with Bed File (keeping a read and its mate)? 0 I have a Bam file for which I want to REMOVE reads overlapping with a given Bed file (so keep all other reads/alignments). I also want to make sure reads and their mates are always…

Forum:Can not get bcftools norm to join biallelics into a multiallelic. 0 is this the right way to use bcftools to join/merge biallelic records into a multiallelic? If so, it is not working. No errors but it gives me the same file with my command added to the headers. Example…

What are some alternatives? When comparing bwa-mem2 and htslib you can also consider the following projects: minimap2 – A versatile pairwise aligner for genomic and spliced nucleotide sequences bowtie2 – A fast and sensitive gapped read aligner genozip – A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF,…

Does running samtools sort in parallel result in unexpected output due to temporary file conflicts? 0 Hi I am runing samtools sort on my cluster with a preinstalled version (may outdate), its version is $ samtools –help Program: samtools (Tools for alignments in the SAM format) Version: 1.3.1 (using htslib…

Tutorial:How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04 2 Just thought I would contribute this since figuring it all out was a super confusing process consisting of a few hundred google searches. It’s likely it was just me, but maybe there are a few other people like me…

Fasta file and GTF file for STAR alignment 3 Hello there, The top-level fasta file will include chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions. See more here: ftp.ensembl.org/pub/release-92/fasta/mus_musculus/dna/README. If you are only looking for reference genome assembly chromosome level sequences then use the primary_assembly.fa file. The…

Provided by: samtools_1.10-3_amd64 NAME samtools index – indexes SAM/BAM/CRAM files SYNOPSIS samtools index [-bc] [-m INT] aln.bam|aln.cram [out.index] DESCRIPTION Index a coordinate-sorted BGZIP-compressed SAM, BAM or CRAM file for fast random access. (Note that this does not work with uncompressed SAM files.) This index is needed when region arguments are…

samtools markdup in Rsamtools 2 I’d like to use Rsamtools to remove duplicate reads from a bam file. I’m looking for a solution similar to samtools markdup -r -s in.bam out.bam. Can anyone tell me how to do this in R, preferably with Rsamtools? But other solutions are also fine…

htslib/c what is the correct way to use bgzf_thread_pool ? 1 I try to split fastq files into ‘N’ chunks using a simple CC program and htslib-C . It works fine: ./split2file -o TMP S1.R1.fq.gz S1.R2.fq.gz -n 10 but when I use a thread pool ( As far as I…

samtools calmd and original base quality 0 Hi, I’m currently trying to use samtools calmd to calculates MD and NM tags for my bam files, I noticed that the typical usage mentioned in the documentation (www.htslib.org/doc/samtools-calmd.html) is samtools calmd -bAr aln.bam > aln.baq.bam and the params -b -A -r means：…

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…

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…

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…

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  …

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  …

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…

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…

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…

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…

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…

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…

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…

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”…

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…

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…

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…

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….

Zenodo DOI Badge DOI 10.5281/zenodo.5797825 Markdown [](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

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…

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…

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…

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…

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…

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…

Ask questionsBam indexing error-the samtools index command for just 1 chromosome is also not working in this case, the following error is showing [E::hts_idx_push] Region 536871288..536871299 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 samtools index: failed to create…

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…

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…

  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…

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…