[Samtools-help] SAMtools and HTSlib release 1.22.1

SAMtools and HTSlib version 1.22.1 are now available from GitHub and SourceForge. This fixes crashes that could happen when reading malformed CRAM files, or when writing files with very long secondary alignments as CRAM 3.1. It also fixes some issues that caused builds to fail on some older plat

[Samtools-help] Release 1.22

Samtools (and HTSlib and BCFtools) version 1.22 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.22 https://github.com/samtools/samtools/releases/tag/1.22 https://github.com/samtools/bcftools/releases/tag/1.22 https://sourceforge.net/projects/samtoo

Re: [Samtools-help] mpileup differences between samtools and bcftools [EXT]

On Tue, 22 Oct 2024, Nate Brown wrote: I'm running a pipeline that uses a very old version of samtools mpileup version 1.6. When we switched to the more modern bcftools mpileup version 1.16 we noticed that the data changed slightly, for example some of the lower frequency calls that used to hav

[Samtools-help] Release 1.21

Samtools (and HTSlib and BCFtools) version 1.21 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.21 https://github.com/samtools/samtools/releases/tag/1.21 https://github.com/samtools/bcftools/releases/tag/1.21 https://sourceforge.net/projects/samtool

[Samtools-help] Release 1.20

Samtools (and HTSlib and BCFtools) version 1.20 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.20 https://github.com/samtools/samtools/releases/tag/1.20 https://github.com/samtools/bcftools/releases/tag/1.20 https://sourceforge.net/projects/samto

[Samtools-help] SAMtools release 1.19.2

Samtools release 1.19.2 is now available from GitHub and SourceForge. It fixes an error in 1.19.1 that broke filtering on unordered BED files. https://github.com/samtools/samtools/releases/tag/1.19.2 https://sourceforge.net/projects/samtools/ ---

[Samtools-help] SAMtools and HTSlib release 1.19.1

Samtools and HTSlib release 1.19.1 are now available from GitHub and SourceForge. This release fixes a regression in version 1.19 that caused written CRAM files to be much bigger than necessary. It also fixes a number of other bugs listed below, including one that could cause crashes or incorrec

[Samtools-help] Release 1.19

Samtools (and HTSlib and BCFtools) version 1.19 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.19 https://github.com/samtools/samtools/releases/tag/1.19 https://github.com/samtools/bcftools/releases/tag/1.19 https://sourceforge.net/projects/samtool

[Samtools-help] Release 1.18

Samtools (and HTSlib and BCFtools) version 1.18 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.18 https://github.com/samtools/samtools/releases/tag/1.18 https://github.com/samtools/bcftools/releases/tag/1.18 https://sourceforge.net/projects/samtoo

[Samtools-help] Release 1.17

Samtools (and HTSlib and BCFtools) version 1.17 is now available from GitHub and SourceForge. https://github.com/samtools/htslib/releases/tag/1.17 https://github.com/samtools/samtools/releases/tag/1.17 https://github.com/samtools/bcftools/releases/tag/1.17 https://sourceforge.net/projects/samtoo

[Samtools-help] SAMtools release 1.16.1

Samtools version 1.16.1 is now available from GitHub and SourceForge. This release fixes some bugs in the new template-coordinate sort feature. https://sourceforge.net/projects/samtools/ https://github.com/samtools/samtools/releases/tag/1.16.1 The main changes are listed below:

[Samtools-help] Release 1.16

Samtools (and HTSlib and BCFtools) version 1.16 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.16 https://github.com/samtools/samtools/releases/tag/1.16 https://github.com/samtools/bcftools/releases/tag/1.

Re: [Samtools-help] bcftools isec retain duplicates [EXT]

On Tue, 2 Aug 2022, Thomas Juettemann wrote: I came across a "transcript-based" VCF file, meaning a variant can be present multiple times but belonging to a different transcript. See "FIle 1" below as an example. I am finding myself in the unfortunate situation of having to intersect ("File 2")

[Samtools-help] Release 1.15.1

Samtools (and HTSlib and BCFtools) version 1.15.1 is now available from GitHub and SourceForge. This fixes bugs found in the 1.15 release. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.15.1 https://github.com/samtools/samtools/releases/tag/1.15.1 ht

[Samtools-help] Release 1.15

Samtools (and HTSlib and BCFtools) version 1.15 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.15 https://github.com/samtools/samtools/releases/tag/1.15 https://github.com/samtools/bcftools/releases/tag/1.

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT]

On Wed, 19 Jan 2022, Sabine van Schie wrote: Dear Robert, What a coincidence you saw my message and recognized the file, thank you for your time. The md5 sum and the ChrXI header match with what you obtained using the original file. With the reference genome used for alignment the error disapp

Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice

On Tue, 18 Jan 2022, Sabine van Schie wrote: Hi all, I used samtools index to index cram files and tried to view the data in the Integrated Genomic Viewer (https://software.broadinstitute.org/software/igv/ ). The samples are whole-genome sequencing data from S. cerevisiae. We have downloaded t

[Samtools-help] Release 1.14

Samtools (and HTSlib and BCFtools) version 1.14 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.14 https://github.com/samtools/samtools/releases/tag/1.14 https://github.com/samtools/bcftools/releases/tag/1.

[Samtools-help] Release 1.13

Samtools (and HTSlib and BCFtools) version 1.13 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.13 https://github.com/samtools/samtools/releases/tag/1.13 https://github.com/samtools/bcftools/releases/tag/

[Samtools-help] Release 1.12

Samtools (and HTSlib and BCFtools) version 1.12 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.12 https://github.com/samtools/samtools/releases/tag/1.12 https://github.com/samtools/bcftools/releases/tag/1.

[Samtools-help] Release 1.11

Samtools (and HTSlib and BCFtools) version 1.11 is now available from GitHub and SourceForge https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.11 https://github.com/samtools/samtools/releases/tag/1.11 https://github.com/samtools/bcftools/releases/tag/1

Re: [Samtools-help] Filter on integer tags not working [EXT]

On Fri, 11 Sep 2020, Benjamin Audit wrote: Using filtering option "-d NM:0" returned an empty set of alignments. A few tests suggest that this is always the case for integer tags, while filtering works as expected for tags of type string (Z). (I use samtools Version: 1.10 (using htslib 1.10.2)

Re: [Samtools-help] SAM to BAM permission denied [EXT]

On Mon, 20 Apr 2020, Pedro Hollanda Carvalho wrote: Hi, could anyone help me with this? I'm trying to convert SAM to BAM using samtools view and I have the following error message $ sudo samtools view -bS Kp01.sam > Kp01.bam -bash: Kp01.bam: Permission denied Judging from the error message,

[Samtools-help] Release 1.10

Samtools (and HTSlib and BCFtools) version 1.10 is now available from GitHub and SourceForge https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.10 https://github.com/samtools/samtools/releases/tag/1.10 https://github.com/samtools/bcftools/releases/tag/1.

Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT]

On Mon, 17 Jun 2019, Karina Borlaug wrote: I tried this command instead: $samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -B -f Hg19.fasta sample.bam But got the exact same output as without the -B option. However as you point out it might be more valuable to keep the BAQ. I am trying to e

Re: [Samtools-help] samtools not working with BWA -C flag

On Thu, 14 Mar 2019, Aengus Stewart wrote: Our sequencer is now outputting header lines with the following format @M02212:177:0-CBJHK:1:1101:11456:1264 1:N:0:AGGCAGAA+CTCTCTAT If I use BWA with the -C flag then this header info gets sent to the .sam output file however in the sam->bam

Re: [Samtools-help] Binary files generated on Windows

On Sat, 3 Nov 2018, Remik Ziemlinski wrote: I forked and built the develop branches of htslib and samtools with the msvc compiler v19.13.26132 that's part of VS2017 v15.6.7.  The code changes were fairly trivial.  The makefile modifications were more significant, though.  I think a port to CMa

Re: [Samtools-help] Binary files generated on Windows

On Fri, 2 Nov 2018, Remik Ziemlinski wrote: Hello,  I just ran samtools for the first time on Windows and I saw this warning at the end of its command-line usage: Note: The Windows version of SAMtools is mainly designed for read-only   operations, such as viewing the alignments and generat

Re: [Samtools-help] Command not found

On Sun, 26 Aug 2018, Michael Bunnemeyer wrote: I am unable to use Samtools at present. Each time I try, there is an error stating: "HTSlib development files not found”. This occurs despite the fact that HTSlib- development/INSTALL directory is on the same hard drive. Now several other comm

Re: [Samtools-help] [W::sam_parse1] urecognized reference name

On Sun, 12 Aug 2018, Nowoshilow,Sergej wrote: Dear SAMtools community, I am trying to view the contents of a SAM file using “samtools view”, but unfortunately it fails with the following error message: [W::sam_parse1] urecognized reference name; treated as unmapped I need to use SAMtools to c

[Samtools-help] Release 1.9

Samtools (and HTSlib and BCFtools) version 1.9 is now available from GitHub and SourceForge https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.9 https://github.com/samtools/samtools/releases/tag/1.9 https://github.com/samtools/bcftools/releases/tag/1.9

Re: [Samtools-help] warnings with htslib on MacOS

On Sat, 16 Jun 2018, Richard Durbin wrote: Hello Shane and Rob, I am fixing a problem with pbwt, and now I get link warnings for htslib with a current github install: [Richards-MacBook-Pro:~/tmp/pbwt] rd% make cc -g -O3 -I../htslib pbwtMain.o pbwtCore.o pbwtSample.o pbwtIO.o pbwtMatch.o pb

Re: [Samtools-help] samtools view -L option

On Mon, 16 Apr 2018, RITSUKO OIKAWA wrote: Samtools does have an option to *filter* the reads according to regions specified in the BED format. $ samtools view -hL chr22_21804028_ref.Gene.bed PLCPRF5bis44.sam > PLCPRF5bis44.filtered.sam [E::sam_parse1] missing SAM header [W::sam_read1] Parse e

[Samtools-help] Release 1.8

Samtools (and HTSlib and BCFtools) version 1.8 is now available from GitHub and SourceForge https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.8 https://github.com/samtools/samtools/releases/tag/1.8 https://github.com/samtools/bcftools/releases/tag/1.8

[Samtools-help] BCFtools 1.7

BCFtools 1.7 is now available from GitHub and SourceForge (Samtools and HTSlib 1.7 were previously released on 26th January). https://sourceforge.net/projects/samtools/ https://github.com/samtools/bcftools/releases/tag/1.7 The main changes are listed below:

Re: [Samtools-help] sort sam file using samtools sort

On Wed, 31 Jan 2018, Yogesh Gupta wrote: Can I use samtools sort to sort sam file by read name directly? samtools sort -O sam -n -o sample.sort.sam sample.sam Yes, that should work. I am using samtools version 1.4 I'd recommend upgrading to the most recent version (1.7). Sort has had a

[Samtools-help] (no subject)

Samtools (and HTSlib) version 1.7 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.7 https://github.com/samtools/samtools/releases/tag/1.7 BCFtools 1.7 will follow soon. The main changes are listed below:

Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently (fwd)

Sorry, forgot to CC this to the list... -- Forwarded message -- Date: Tue, 26 Dec 2017 13:18:06 + From: rmd To: Hu Jing Subject: Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently On 2017-12-26 00:56, Hu Jing wrote: Recently we ran into an is

Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1

On Fri, 17 Nov 2017, VIB | Stephane Plaisance wrote: Thanks Robert for the rapid feedback, I tried but it die not fix it. I seem to have an issue with gcc Ah, sorry. My instructions were wrong. It should have been: ./configure CPPFLAGS='-I /opt/local/include' This is what happens when you

Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1

On Fri, 17 Nov 2017, VIB | Stephane Plaisance wrote: I did install before but after upgrading to high Sierra I am lacking some dev dependencies (Xcode is installed) I tried installing xz using macport and got the error below (there is no port with -dev) xz -V xz (XZ Utils) 5.2.3 liblzma 5.2.3

Re: [Samtools-help] help installing samtools

On Tue, 14 Nov 2017, Ricardo Fong Zazueta wrote: Hello, i am a new samtools user and i am having trouble installing the package on my ubuntu 16.4 virtual machine (installed in a windows 7 host machine). I have read the INSTALL script written in the samtools main folder after downloading sam

Re: [Samtools-help] samtools truncated file and Exec format error

On Wed, 8 Nov 2017, Susan Fairley wrote: Thanks for letting me know about this. I’ve had a (very) quick look and the samtools view -H command is working for me with v1.2. [alignment]:samtools Program: samtools (Tools for alignments in the SAM format) Version: 1.2 (using htslib 1.2.1) [alig

Re: [Samtools-help] samtools truncated file and Exec format error

On Wed, 8 Nov 2017, Tommy Carstensen wrote: To samtools-help, 1) I am trying to convert a cram to bam with samtools view v1.5, but eventually I get the error below for some of the files, whereas others are successfully converted: Block CRC32 failure [main_samview] truncated file. Has anyone

[Samtools-help] Release 1.6

Samtools (and HTSlib and BCFtools) version 1.6 is now available from GitHub and SourceForge https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.6 https://github.com/samtools/samtools/releases/tag/1.6 https://github.com/samtools/bcftools/releases/tag/1.6

Re: [Samtools-help] Using Samtools as a Dependency: Getting a large amount of binary in terminal window

On Tue, 11 Jul 2017, Amelia Lawrence wrote: I am currently using a python package methylpy, which uses samtools as a dependency. When calling samtools in the package script I'm getting a binary output in my terminal window. When viewing the package code I see two different methods of calling sam

Re: [Samtools-help] Zero Length Reads in SAM

On Mon, 16 Jan 2017, Colin Hercus wrote: > Sometimes we get reads to align that have been trimmed to zero length and > I'm wondering how these should be represented in SAM format. > > Here's a pair as reported by Novoalign that had been trimmed by cutadapt > and one read of the pair is zero length

Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header

On Wed, 4 Jan 2017, John Marshall wrote: > TL;DR i.e. what Rob said. But note that when you output SAM with >samtools view, samtools appends basic @SQ headers if there aren't already >any. So Rob's `samtools view -H ... | grep '^@SQ'` will display some >headers whether the file contains text

Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header

On Tue, 3 Jan 2017, Holbrook J. wrote: Dear Samtools help members Happy 2017! I would be very grateful for your help: I am trying to manipulate .bam files created by ernebs5 (http://erne.sourceforge.net) aligning against hg19. I am running samtools 1.3.1 I have ~ 1.5 mil singleton and ~ 100

[Samtools-help] faidx index caching

I'm currently looking at htslib issues #375 and #380, which both involve how htslib downloads remote index files. For example, running: samtools faidx ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa chr1:100-10