Tag: vcfutils

Samtools Bcf To Vcf Problem 1 Hi I have a bcf file generated using bcftools(samtools), which I further wanted to convert to vcf format. I used the following command: bcftools view ../bcf/test.bcf | vcfutils.pl varFilter -D 8000 > test.vcf The corresponding vcf file only generated the header and not 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…

samtools mpileup -uf reference.fasta sorted_aligned_reads.bam | bcftools call -c | vcfutils.pl vcf2fq > consensus.fastq Here’s a breakdown of the command: samtools mpileup: Generates a pileup of aligned reads at each position in the reference genome. -u: Output in uncompressed BAM format. -f reference.fasta: Specifies the reference genome in FASTA format….

Maximum Read Depth 3 Hi, I wish to get the variants of my sequencing data using Samtools (vcfutils). For this I need to specify the maximum read depth in VarFilter function. I have no information of this from my Data. Can anybody tell me, how should I approach to its…

Difference between vcf2fq and bcftools consensus 1 Hi everybody, I’m working for generate consensus sequence and I’m interogating myself about the differences of work process between bcftools consensus and vcf2fq from vcfutils.pl. In the one hand, thanks to vcf2fq, I can generate consensus sequence with the following command: bcftools mpileup…

Change sequence ID in fastq file generated by bcftools mpileup 0 Hi everobody ! I’m currently work on a HHV8 genetic study and I face to an issue with my bcftools command. Indeed, I want to generate consensus sequences thanks bcftools mpileup command and bam files. However, all ID get…

Hi everyone, Recently, I have been using bcftools consensus to generate consensus sequence as the following commands: bcftools mpileup -Ou -f ref.fa in.bam | bcftools call -Ou -mv –ploidy 1 | bcftools norm -f ref.fa -Oz -o norm.vcf.gz bcftools index norm.vcf.gz bcftools consensus -f ref.fa -o consensus.fa norm.vcf.gz However, the…

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  …

Name Last modified Size Description Parent Directory   –   HmmGlocal.java 2014-08-01 09:48 9.0K   ace2sam.c 2016-05-10 08:11 11K   blast2sam.pl 2017-09-14 10:20 5.2K   bowtie2sam.pl 2014-08-18 14:29 3.3K   export2sam.pl 2014-08-01 09:48 18K   interpolate_sam.pl 2014-08-18 14:29 6.0K   maq2sam.c 2017-12-12 11:10 7.2K   md5fa.c 2017-07-24 09:15 2.8K  …

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…

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…

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

Vcfutils error code 20-08-2021 code at line (I think) just to get it to write a proper fq. Second issue is this error: substr outside of string at /usr/local/bin/object91.ru line We can do this in a single…