On 27 May 2014, at 10:58, Wolfgang Maier
wrote:
> On 22.05.2014 20:59, Kate Im wrote:
>> the number of unmapped read (estimated by
>> subtracting the reported number of mapped reads from the reported number
>> of total reads) is always higher than the number of sequences with an "*"
>> in the thi
On 1 Jul 2014, at 16:06, Marcel Martin wrote:
> Interestingly, at least in my samtools version (0.1.19-96b5f2294a,
> Ubuntu 14.04), the EOF marker check is also done (and fails) when you
> pipe in a BAM file from stdin:
>
> $ samtools view -b merged.bam | samtools view - > /dev/null
> [bam_head
On 23 Jul 2014, at 10:58, Dan Bolser wrote:
>
> I like these comments:
[...]
>
>"Hopefully 2 Gbp [per chromosome - JM] suffices for most species that
> people are
> interested in." - John Marshall. [Somewhat taken out of context, see below -
> JM]
&
On 28 Jul 2014, at 20:49, Sullivan, Catherine
wrote:
> Sorry new to programming. Just wrote my first perl script, and using
> samtools piped into grep to get an calls at a specific location. However,
> each time it run the script and it runs samtools, I get this in STDOUT:
>
> [mpileup] 1 s
Major new versions of samtools and associated tools have been released.
Significant changes include:
* support for CRAM, a sequence data file format with better compression than BAM
* support for BCF v2, a binary equivalent to the VCF format that is more
flexible than the old BCF1
* bcftools ha
On 19 Aug 2014, at 17:33, Rieux, Adrien wrote:
> I’m using the new SAMtools and BCFtools versions (v1.0).
> Is there a manual for SAMtools v1.0 ? I can find one for BCFtools
> (http://www.htslib.org/doc/) but not for SAMtools and it looks like some
> commands changed (compared with the previous
On 5 Sep 2014, at 06:52, Adam Skarshewski wrote:
> Running into a problem with samtools 1.0 sort, specifically the merging
> phase. It's very slow compared to the previous version. I have a 965MB bam
> file (which is already sorted)
Does your BAM file have rather a lot of reference sequences?
On 11 Sep 2014, at 03:00, Dario Strbenac wrote:
> -l INT Set compression level, from 0 to 9 [-1]
>
> If valid values range from 0 to 9, why is the default -1 ? Also, do higher
> values correspond to more compression ? The documentation is not explicit as
> to how the numbers relate to the a
On 17 Sep 2014, at 20:53, Ni Huang wrote:
> in this BAM, the primary and the supplementary alignment of each read are
> mis-labeled as a read pair (the 7th and 8th column). I had a samtools fixmate
> (version 0.1.19) step before Picard Markduplicates, which might be the real
> culprit, as the e
New 1.1 versions of htslib, samtools, and bcftools have been released. These
are minor bug-fix releases, and include the following notable fixes and new
functionality compared to 1.0:
* Samtools fixmate and flagstat now consider supplementary reads
* Sorting BAM files with thousands of referenc
On 25 Sep 2014, at 16:29, Nils Homer wrote:
> I see that the "samtools view -X" option is missing. This option is
> incredibly useful for debugging SAM/BAM (and now CRAM) records. It seems
> that this option was lost in the newest release. Would it be possible to add
> that back in?
The hex
On 7 Oct 2014, at 00:08, Derek M.
wrote:
> I've installed samtools-1.1 and htslib-1.1.
> [...]
> $ samtools index SRR794854.bam SRR794854.bai
> Samtools-htslib-API: bam_index_build2() not yet implemented
> Aborted (core dumped)
bam_index_build2() is an entry point to the indexing code that lets
On 31 Oct 2014, at 12:38, Nick Loman wrote:
> Latest build of samtools (1.1) mpileup core dumps with the following file
> (produced with latest BWA and samtools on nanopore data) in -g (BCF) or -v
> (VCF) mode, e.g..
>
> samtools mpileup -Q 0 -f NC_000913.fna -g Ecoli_R73_2D.bam
[...]
> http://
On 6 Nov 2014, at 01:28, Mark Ravinet wrote:
> Grepped lines from a typical header are as follows:
>
>> @PG ID:GSNAPPN:gsnapVN:2013-11-27 CL:gsnap -d stick_ref
>> --maxsearch=10 -M 0 -m 5 -t 6 -n 1 -A sam --quiet-if-excessive
>> --terminal-threshold=10 -i 2 ./samples_081014/C
On 6 Nov 2014, at 19:15, Shana Burrowes wrote:
> I am trying to install Samtools and I keep getting the error below. What can
> I do to fix it?:
>
> ./libbam.a(bam_import.o): In function `ks_getuntil':
> /home/stine/samtools-0.1.1/bam_import.c:12: undefined reference to `gzread'
[etc]
Your prob
On 13 Nov 2014, at 12:23, Karel Břinda wrote:
> I observe a strange problem and I am not able to find out what is the exact
> reason of it. When I use "samtools mpileup | another_program", samtools
> return error code 141.
When a Unix shell reports that a command has an exit status greater than
On 19 Nov 2014, at 17:47, Peter Cock wrote:
> I have no idea what 'minQLen' was short for, unless the Q
> was a typo?
It would be Minimum Query Length, where query is a synonym for read (imagine
you were an aligner being asked to map a read...). This is also what SAM/BAM's
QNAME field stands f
On 3 Dec 2014, at 18:39, Radhouane Aniba wrote:
> I noticed that samtools is not managing exit code for its programs the same
> way
This is in general https://github.com/samtools/samtools/issues/51 . It takes
somewhat disproportionate effort to fix all these as each instance reflects a
separa
On 4 Dec 2014, at 17:52, Kevin wrote:
> remove this email from the list….I have another one I am having this sent to
> …so this is a duplicate
Presuming you are asking for your @mho.com email address to be unsubscribed
from the mailing list, I have done so. If you meant something else, please
On 17 Dec 2014, at 14:39, Will McLaren wrote:
> A bit of googling led me to find that the order of included libs in the
> Makefile can cause issues, so I changed it:
>
> sed -i.bak "s/-lz -L.. -ltabix/-L.. -ltabix -lz/" Makefile.PL
[...]
> If this doesn't affect other systems (which in my tests
New 1.2 versions of Samtools and BCFtools and a 1.2.1 version of HTSlib have
been released. These provide improvements in CRAM support and variant calling,
as well as a number of bug fixes and speed improvements. (The 1.2 HTSlib
release was immediately superseded by 1.2.1 when a compatibilty is
On 11 Feb 2015, at 13:12, Sendu Bala wrote:
> I'm using the latest samtools (1.1) and picard (1.128).
>
> If I make a bam using the -u option of eg. calmd, it now creates a raw
> uncompressed bam (as opposed to a bgzip bam with compression level 0, which
> is what samtools v0 did).
As Peter co
On 21 Feb 2015, at 01:43, Adam Birnbaum wrote:
> I’ve been looking for information and documentation on CSI format, and found
> only this one page on the record format and binning algorithms:
> http://samtools.github.io/hts-specs/CSIv1.pdf.
That CSI document at http://samtools.github.io/hts-sp
On 11 Mar 2015, at 14:24, Bob Harris wrote:
> That's one seriously broken grammar that considers "1750M" to mean 175
> but thinks "1.75G" means 1.
You are not wrong. Coincidentally we've been working on improving ways to
specify numbers in htslib for a while, and can probably take advantag
On 13 May 2015, at 12:17, Kanterakis, Efstathios
wrote:
> bgzip chr1_h.vcf
> bgzip chr2.vcf
> cat chr1_h.vcf.gz chr2.vcf.gz > test.vcf.gz
...i.e., constructs test.vcf.gz with many BGZF blocks, including an EOF trailer
block from each of chr1_h.vcf.gz (in the middle of test.vcf.gz) and chr2.vcf.
On 14 May 2015, at 22:02, Heng Li wrote:
> A historical background. Terminating at EOF was intended initially. The idea
> was to allow a BAM footer for extra information, such as the index.
> Nonetheless, we have not gone much further with this idea.
Emails of the time [1] suggest it was floate
On 15 Jun 2015, at 17:46, Lo, Chien-Chi wrote:
> Samtools (v1.2) merge doesn’t output any file of my two bam file and no
> message throwing out. It just hang there and reserved ~2.0g memory. However,
> 0.1.18 version finish the merging in ~2 mins.
>
> The two sorted bam files are 449M and 44
On 6 Jul 2015, at 12:04, ma.meyerh...@freenet.de wrote:
> I read something about the -C parameter and retried with
> bwa mem -aHMpP instead of bwa mem -aCHMpP, but the header looks the same:
>
> samtools view -H ./output/KMT/9557-FGS-R.sam
> @SQSN:B.FR.1983.HXB2-LAI-IIIB-BRU.K03455LN:9719
On 27 Jul 2015, at 17:36, Patrick Reilly
wrote:
> I'm using BWA v0.7.12-r044 and samtools v1.2-99-ge2bb18f
> [...] sorting with output as BAM or SAM results in the loss of the RG header,
> while the alignment RG tags remain (thereby corrupting the SAM/BAM file,
> according to GATK).
>
> I've a
On 26 Aug 2015, at 21:02, Samantha Klasfeld wrote:
> I am using samtools mpileup and I was wondering what a reference skip is. I
> got output that showed there were nucleotides that skipped the reference.
> Then, when I compared the reads to the reference I noticed that they were
> perfect matc
On 7 Sep 2015, at 13:49, Tom Adlerteg wrote:
> We are currently working on a tool for statistical analysis of substitutions
> and indels. As we see it is no longer supported to be able to print mapping
> qualities as a separate column when using samtools mpileup. This
> functionality would be m
On 10 Sep 2015, at 21:54, Terry Casstevens wrote:
> If you use bgzip to zip an already gzipped file, does that result in a
> correctly bgzipped file?
>
> Or should you first ungzip the file and then bgzip?
Your tools are expecting a file with a single layer of bgzipping, so as Peter
noted you w
On 16 Sep 2015, at 22:24, Brendan Kohrn wrote:
> I found the following issue in the output from samtools mpileup (-f), with a
> single bam file input:
>
> gi|255961284|ref|NC_011713.2| 140 G 1 ,$ C
> gi|255961284|ref|NC_011713.2| 149 A 0
> gi|255961284|ref|NC_0
On 24 Sep 2015, at 09:06, Maria Sutton wrote:
> I am preparing my fasta file so I can apply it to HaplotypeCaller. At the
> stage where I use samtools faidx tmp.fasta I'm getting segmentation fault
> (core dumped). At first it specified the errors so I got rid of the blank
> lines in the sequen
On 3 Oct 2015, at 23:52, Pär Larsson wrote:
> Sorry to bother you with a question relating to an older discussion
> (http://sourceforge.net/p/samtools/mailman/message/34109200/). John Marshall
> expressed concerns that removal of the 28 byte EOF block from bgzip archives
> would b
On 4 Nov 2015, at 21:25, Tagliamonte,Massimiliano S
wrote:
> I am trying to add an annotation column to my vcf file, after calling
> variants with the Samtools 1.x pipeline. I am using bcftools annotate, but I
> keep getting the same error regarding one of the headers:
> Could not parse the hea
Hello Michael,
On 5 Nov 2015, at 16:56, Michael Nuhn wrote:
> I am using samtools 1.2. When I run the index command like this:
>
> /software/ensembl/funcgen/samtools index
> /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam
>
> samtools ins
On 19 Nov 2015, at 10:49, Ivo Palli wrote:
> In file included from bam_cat.c:44:
> ../htslib/htslib/cram.h:391: error: expected declaration specifiers or
> ‘...’ before ‘va_list’
> make: *** [bam_cat.o] Error 1
>
> This can be solved by putting
>
> #include
>
> in htslib/htslib/cram.h
Indeed
On 1 Dec 2015, at 12:20, hgong wrote:
> I am new to the samtools. I install samtools 1.2 as it's directed and it
> succeeds. when I try compile your example of samtools C :
>
> http://samtools.sourceforge.net/sam-exam.shtml
This is an old web page containing a program demonstrating using the ol
On 7 Dec 2015, at 21:47, Claudio Alberti wrote:
> I am implementing a parser that is able to read the BAM file in pairs so
> whenever I read a record where pos < mpos I search for the mate and I
> create a pair structure.
> Once I find the mate I have to roll back to the second read and continue
On 8 Dec 2015, at 13:56, Claudio Alberti wrote:
>
> It seems that bgfz_seek and bgzf_tell can work as well, do you see any issue
> with them?
It would be a similar situation to that noted in that September BCF / VCF.GZ
thread, though you are in a better position due to the legacy existence of
New 1.3 versions of Samtools, BCFtools, and HTSlib have been released. These
have numerous bug fixes, improvements, and new commands. The changes are too
numerous to list here, but we would particularly like to draw your attention to
these three items:
* The old way of invoking the samtools s
On 16 Dec 2015, at 10:06, Stephane Plaisance | VIB |
wrote:
> When trying compile the new release, I get the following error
>
> $ gcc -pthread -rdynamic -o samtools bam_index.o bam_plcmd.o sam_view.o
> bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o
> bam_rmdupse.
On 31 Dec 2015, at 10:15, Robert May wrote:
>
> I have just installed cygwin64 on a Windows10 machine and have run into
> problems with installing as below. Any assiance appreciated.
[...]
> checking whether the C compiler works... no
> configure: error: in `/usr/local/bin/htslib-1.3':
> configu
On 27 Jan 2016, at 15:16, Claudio Alberti wrote:
> I'm looking for a way to programmatically get the number of reads
> contained in a BAM file which are mapped on one of the used references.
> I'm currently using htslib and I'm wondering if any API is available to
> do that.
Look at hts_idx_get
On 16 Feb 2016, at 11:44, Stephane Plaisance
wrote:
> I get the following on OSX 10.10.5
[...]
>
> gcc: error: unrecognized command line option '-rdynamic'
See https://sourceforge.net/p/samtools/mailman/message/34699333/ ; most GCC
compiler drivers understand this option, but apparently not t
On 16 Feb 2016, at 15:41, Stephane Plaisance
wrote:
> gcc: error: -compatibility_version only allowed with -dynamiclib
[...]
> libhts.dylib: $(LIBHTS_OBJS)
> $(CC) -Wl,-export_dynamic -install_name
> $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version
> $(NUMERIC_VERSION) -compati
On 16 Feb 2016, at 23:22, Friedman, Ryan wrote:
> The entire pipeline works fine up until rmdup where it immediately results in
> a segmentation fault.
>
> What's particularly interesting is that this seg fault only occurs in some
> files. I originally thought this had something to do with size
On 22 Feb 2016, at 01:05, William Hsiao wrote:
>
> I’m trying to install Samtools 1.3 on a RHEL 6.2 system. I seemed to be able
> to install htslib 1.3 but as I try to install samtools 1.3 I encountered the
> following error when I type:
This gzopen64() problem seems to be a long-standing pro
On 22 Feb 2016, at 08:34, William Hsiao wrote:
> Thanks for your help. Below is the output you requested. Btw, I was able to
> get Samtools to compile by issuing "sudo make LDFLAGS="-L/usr/local/lib”,
> where a newer version of zlib (libz.so.1.2.8) is available. Could it be that
> the versio
On 23 Feb 2016, at 21:00, William Hsiao wrote:
> Thank you so much for solving the problem for me. I definitely learned
> something. I’m trying to figure out where did you see the /usr/lib64/
> specified. I was trying to look for a second copy of libz.so that might
> cause a conflict but cou
On 4 Mar 2016, at 12:11, Ryan Kevin wrote:
> In version 0.1.19 of bcftools view there is the setting:
>
> -N which is defined as Skip sites where the REF field is not A/C/G/T
>
> I am currently running version 1.2 of bcftools and I realised that I still
> have -N set when calling bcftools call.
On 16 Mar 2016, at 11:20, Wybouw, Nicky wrote:
> I get this output
>
> [E..hts_open_format] fail to open file '.bam'
> [mpileup] failed to open '.bam': Value too large for defined data type
>
> The input BAM files worked fine using the old version and are only 8.2GB big.
You are running samtool
On 4 Apr 2016, at 08:19, Kaamesh Kamalaaharan wrote:
> Hi, i downloaded tabix 0.2.6 from the sourceforge page, but when running the
> tabix file, it shows version as 0.2.5.
The code in that tarball corresponds to the following commit:
https://github.com/samtools/tabix/commit/8c13556fd2
On 4 Apr 2016, at 21:40, Shinn Kondo wrote:
> I was using version 1.1 of samtools mpileup, but it exited abnormally
> after the following warning: "[bam_plp_destroy] memory leak: 45.
> Continue anyway."
>
> Reading a post about the same warning in
> https://www.biostars.org/p/173354/, I reali
On 20 Apr 2016, at 13:50, Anne Philippi wrote:
> I find a bug when I used fastq option of samtools:
> anne$ samtools fastq -nO input_sorted.bam -1 output_1.fastq -2 output_2.fastq
> Segmentation fault
This is most likely a bug that strikes when processing an alignment record
doesn't have an OQ a
New 1.3.1 versions of Samtools, BCFtools, and HTSlib have been released. This
is mainly a bug fix release, fixing a number of bugs and issues in December's
1.3 release. In particular:
* Improved management of samtools sort temporary files. Running several
separate "... | samtools sort | ..."
On 28 Apr 2016, at 15:03, Tagliamonte,Massimiliano S
wrote:
> ... I'm ashamed to ask... what is the dash ( "-" )before redirecting the
> output?
> i.e.: flagstat - > myfile.stats. If I don't use the dash, it gives me a
> broken pipe error. I did some googling, still not sure of its meaning.
It
On 3 May 2016, at 19:11, Dan Hyatt wrote:
>
> I am installing samtools 1-3-1, the newest version released last week
> and trying to compile it on Centos (redhat) 6.7
[...]
>
> I checked and verified that I installed ncurses and devel-ncurses as
> seen at the bottom.
>
> google did not indica
On 8 May 2016, at 17:27, Peter Chovanec wrote:
> Why doesn't this work:
>
> samtools view sample.bam 2:33050509-33154206 -U without-region.sam
>
> or
>
> samtools view -b sample.bam 2:33050509-33154206 -o other_stuff.bam -U
> without-region.bam
You don't say what you were expecting to have ha
On 27 May 2016, at 06:14, Peter Johansson wrote:
> Seems the problematic entry had a negative QUAL (-2147480064), which looks
> very suspicious. Need to go upstream and look for the source of that.
QUAL is Phred-scaled, so by definition valid values are non-negative. So the
upstream source mig
On 18 May 2016, at 18:23, Arti Tandon wrote:
> I am using bcftools-1.3.1/htslib-1.3.1/tabix* to index the dbNSFP file to be
> used by the program SnpSift, using the following commands and am getting an
> error:
>
> $ (head -n 1 dbNSFP3.2c_variant.chr1 ; cat dbNSFP3.2c_variant.chr* | grep -v
>
On 10 Jun 2016, at 15:44, CHANE-WOON-MING Béatrice (VIE)
wrote:
> I'm currently trying to install samtools-1.3.1 on an iMac 10.6.8. Everything
> seems to be ok after the "./configure" command, but I'm facing with the
> following make error and I didn't manage to find a related thread on the
>
On 22 Jul 2016, at 21:49, Annie Cowell wrote:
> samtools mpileup -C50 -Bug -t AD -Q10 -f my.fasta sample.bam | bcftools call
> -mv -Ov > my.vcf
>
> However, I am getting unusual bases for a couple of indels in the reference
> field, such as W (as below) and R.
>
> AAKM0165 8883.
On 27 Jul 2016, at 15:34, Adam Witney wrote:
> I am upgrading an analysis from samtools version 0.1.19-44428cd to version
> 1.3.1 (using htslib 1.3.1). I am trying to understand why the pileup changes
> so much in this example
>
> samtools mpileup -s -f genomes/NC_000962.fna alignments/sample-1
On 4 Aug 2016, at 09:04, Þórður Kristjánsson
wrote:
> [unsubscribe]
I have manually unsubscribed from the mailing list.
For anyone else wanting to unsubscribe in the future: the URL at the bottom of
every mail you get from the list has a form for unsubscribing (towards the
bottom of the page
On 22 Aug 2016, at 21:15, Yuelin Zhu wrote:
> I got Segmentation fault whenever doing bcftools index on the following file:
>
> http://gbnci-abcc.ncifcrf.gov/fileman/temp/1348518/geno.TRA.bcf
[...]
>
> $ bcftools index geno.TRA.bcf
> Segmentation fault
Thanks for the bug report. Your file co
On 22 Aug 2016, at 21:22, Thomas W. Blackwell wrote:
>
> I would try downloading the file and indexing your local copy.
That is indeed what the OP did:
>> $ bcftools index geno.TRA.bcf
>> Segmentation fault
> Unless I'm mistaken, nothing in the bcftools documentation
> indicates that it shou
A new 1.3.2 version of HTSlib has been released. This is a very small
increment over 1.3.1 that has been made to address two issues.
When converting directly from CRAM to BAM, for example with `samtools view -b
foo.cram`, the bin field of a small fraction of the reads was previously
calculated
On 26 Sep 2016, at 19:49, Xing Xu wrote:
>
> I am trying to access bam files that are stored on aws S3 storage of my own
> bucket.
>
> I read the release note of samtools and htslib 1.3 support the access to aws
> s3.
>
> Could you provide a detailed instruction that how I can access the bam
On 7 Oct 2016, at 06:24, Juan Daniel Montenegro Cabrera
wrote:
>
> samtools view -bh@ 15 in.sam | samtools sort -T tmp -@ 15 -o out.sorted.bam -
>
> When I try to index the sorted bam file it complains:
>
> samtools index out.sorted.bam
> [E::hts_idx_push] NO_COOR reads not in a single block
On 10 Oct 2016, at 05:35, Juan Daniel Montenegro Cabrera
wrote:
> I did a few test in my spare time. All samtools version from 0.1.19 have the
> same sorting problem, with or without the use of (-@) multiple threads.
> Version 0.1.18 is able to sort the file correctly, but is slower than
> sam
On 18 Nov 2016, at 08:04, 陈然 wrote:
> I met a problem while running samtools faidx command. It shows like:
>
> $ cd /biotool/samtools-1.3.1
> $ ./samtools faidx /data/hg19.fasta
> [fai_build] fail to open the FASTA file /data/hg19.fasta
> Could not build fai index /data/hg19.fasta.fai
>
> I tr
On 21 Nov 2016, at 05:20, 陈然 wrote:
> Thank you very much for your reply. I tried the command you advised me, it
> shows like:
>
> $ cd /biotool/samtools-1.3.1
> $ strace -e open ./samtools faidx /data/hg19.fasta
> [...]
> open("/data/hg19.fasta", O_RDONLY) = -1 EOVERFLOW (Value too larg
On 25 Nov 2016, at 18:09, yincl2013 wrote:
> Recently, when i installed the samtools-1.2 on redhat 6.6 system, i got the
> following problem:
> gcc -pthread -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o
> bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o
> bam_rmdup
On 28 Nov 2016, at 17:51, Sebastian Gregoricchio
wrote:
> I am a student of molecular biology (master degree) and I am studying genome
> assembly against a reference genome.
> I have a, maybe stupid, question: if i have a quality raw in a fastq file
> that starts for symbol @, how can samtools
On 13 Dec 2016, at 23:56, Jacob Ulirsch wrote:
> When I run samtools (v1.3.1) mpileup I am running into some very concerning
> issues. The reference bases for the output pileup file are not in the same
> position as the references in the input fasta. In fact, they appear to be
> oddly shifted.
On 14 Dec 2016, at 11:54, John Marshall wrote:
>
> On 13 Dec 2016, at 23:56, Jacob Ulirsch wrote:
>> Here is output from faidx, showing the correct fasta sequence for these
>> positions:
>>
>> samtools faidx mtDNA.fasta chrM:1330-1340
>>> chrM:1330-1340
On 3 Jan 2017, at 16:21, Holbrook J. wrote:
> I am trying to manipulate .bam files created by ernebs5
> (http://erne.sourceforge.net) aligning against hg19.
> I am running samtools 1.3.1
[...]
>
> samtools sort -T /dev/shm/jostemp -@ 8 -m 4G -o sample1b_paired_sorted.bam
> Sample1b_unmasked.bam
On 5 Jan 2017, at 06:52, Hadas Ner Gaon wrote:
> [unsubscribe]
I have manually unsubscribed from the mailing list.
For anyone else wanting to unsubscribe in the future: the URL at the bottom of
every mail you get from the list has a form for unsubscribing (towards the
bottom of the page), or
On 9 Jan 2017, at 19:05, Madolyn Macdonald wrote:
> I am trying to calculate the mapping statistics of a BAM file. I am using
> SAMtools 1.3.1 and am able to get statistics on the BAM file using samtools
> flagstat. However, when I try samtools stats, which I would like to use, I
> get the foll
On 7 Jul 2017, at 15:39, Gerben Menschaert wrote:
> I’m testing interoperability with existing software tools using our proBAM
> format.
>
> Within the format we added an novel header line, holding information on the
> annotation used:
> @GA AS:ENSEMBL VN:85
>
> The SAM format specifi
On 17 Aug 2017, at 22:38, Yan Li wrote:
> 2. But after I executed the following command, no output file is founded
> > samtools sort -n HBS0001.bam -o HBS0001.namSort.bam
>
> 3. my large log file contains the following non-readable characters
> > head log.0.o183860
> [bam_sort_core] merging fr
On 8 Nov 2017, at 11:36, Tommy Carstensen
mailto:t...@sanger.ac.uk>> wrote:
2) Furthermore, when typing the command below:
samtools view -H
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRC
On 17 Nov 2017, at 15:00, VIB | Stephane Plaisance
mailto:stephane.plaisa...@vib.be>> 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)
[.
On 15 Dec 2017, Brent Pedersen wrote:
> With bam/tabix, we can recognize the stats bin in index 37450
>
> It is not documented how to find this bin for CSI which can have real
> data in 37450.
There exists a draft of a fleshed-out CSI document [1], but alas it still needs
to be rescued from the
On 21 Feb 2018, at 20:05, Nicholas Hill wrote:
> Say my pileup line is this:
> chr373912 A 21 g,,..G,.gGGGgGGg,.Ggg JJ
> So at chr3:73912 the reference was an A. On the forward strand (read1), there
> are 7 guanine base pairs that aligned to the reference sequence at this
> p
On 9 Mar 2018, at 23:56, Nowoshilow,Sergej
mailto:sergej.nowoshi...@imp.ac.at>> wrote:
Apparently, the BAM file is not quite correctly sorted after all. A simple test
samtools view test.sorted.bam | cut -f3 | uniq
proofs that it is indeed the case, since the scaffold IDs are sorted over ~90%
of t
On 16 Apr 2018, at 15:55, Heredia Genestar, Txema wrote:
> HTSLIB 1.5 and 1.8 both have a bug in tabix. It ignores the option for
> 0-based input files.
You are right that there is awkwardness here, but the full story is rather more
involved.
The -0 option is functioning as designed. Like the
On 17 Apr 2018, at 14:40, Heredia Genestar, Txema wrote:
> After further reading the documentation I've finally found the part where it
> explains the -0 option.
>
> I was mistaken and the -0 option is not there if you fancy one or another
> indexing. It is there for the ¿rare? cases where your
On 17 Dec 2018, at 19:08, Rob Thompson wrote:
> I have compiled bcftools with all the required -lcurl -lcrypto -lssl libs.
>
> I can read from a public S3 file fine, but as soon as its make private I just
> get:
> Failed to open FILE.vcf.gz: Permission denied
>
> AWS credentials are set in ~/.a
On 14 Mar 2019, at 15:14, Aengus Stewart wrote:
> I completely understand that and I can fix it. However I am just pointing
> out the current default we are getting from the
> illumina sequencers.
>
> So either
> Illumina needs to conform to the current SAM format in bcl2fastq
> The SAM format
On 22 Apr 2020, at 17:10, Pedro Hollanda Carvalho
mailto:hollandacarva...@gmail.com>> wrote:
I'm unable to perform samtools sort command. Result is a weird buch of symbols
followed by letters and numbers as follows (just a part of it):
yOR�G(��< {`�m�wF�D/�q|lOS�}�H
This weird bunch of symbo
On 8 Jun 2020, at 13:16, Keiran Raine wrote:
>
> Just a quick query. Where does samtools write the temporary files for the
> collate step? Can I assume /tmp or the location defined by $TMPDIR?
At the moment if you want them to appear somewhere in particular other than
/tmp (which is probably
On 10 Mar 2021, at 21:04, Remik Ziemlinski wrote:
> The attached file worked with version 1.9, but is failing with 1.10 and 1.11.
> Is the file valid? Is there a regression after v1.9?
> [...]
> # output from version 1.9
> @HD VN:1.6 SO::unsorted
> @SQSN:referenceLN:5495
Your @HD line i
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