Tag: vcfutils

Samtools Bcf To Vcf Problem

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…

Continue Reading Samtools Bcf To Vcf Problem

131releng-armv7-quarterly][biology/htslib] Failed for htslib-1.17 in build

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…

Continue Reading 131releng-armv7-quarterly][biology/htslib] Failed for htslib-1.17 in build

Generating consensus sequence from bam file

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….

Continue Reading Generating consensus sequence from bam file

Maximum Read Depth

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…

Continue Reading Maximum Read Depth

Difference between vcf2fq and bcftools consensus

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…

Continue Reading Difference between vcf2fq and bcftools consensus

Change sequence ID in fastq file generated by 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…

Continue Reading Change sequence ID in fastq file generated by bcftools mpileup

Bcftools consensus generates mismatched consensus sequence

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…

Continue Reading Bcftools consensus generates mismatched consensus sequence

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

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

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  …

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

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

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

phase_trio.sh | searchcode

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 |…

Continue Reading phase_trio.sh | searchcode

Vcfutils error code

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…

Continue Reading Vcfutils error code