samtools-help

Messages by Date

2018/07/15 Re: [Samtools-help] per-file depth in samtools mpileup Jing meng
2018/07/13 Re: [Samtools-help] Unexpected insert-size distribution given by samtools stats James Bonfield
2018/07/13 Re: [Samtools-help] per-file depth in samtools mpileup James Bonfield
2018/07/13 [Samtools-help] per-file depth in samtools mpileup Jing meng
2018/07/11 Re: [Samtools-help] Unexpected insert-size distribution given by samtools stats James Bonfield
2018/07/09 [Samtools-help] Unexpected insert-size distribution given by samtools stats Dr . Frank Vorhölter
2018/06/22 [Samtools-help] a question about bcftools ??an????
2018/06/18 [Samtools-help] mpileup returns empty vcf file Shreyasi Biswas
2018/06/18 Re: [Samtools-help] warnings with htslib on MacOS Richard Durbin
2018/06/18 Re: [Samtools-help] warnings with htslib on MacOS Robert Davies
2018/06/17 [Samtools-help] warnings with htslib on MacOS Richard Durbin
2018/05/29 [Samtools-help] Question about the reference for samtools Haider, Marlene
2018/05/04 [Samtools-help] Question about BEDTools BEDPE format versus Samtools view -L option Braulio Valdebenito Maturana
2018/05/04 Re: [Samtools-help] Calling indels with noisy reads James Bonfield
2018/05/04 Re: [Samtools-help] Calling indels with noisy reads Jody Phelan
2018/05/03 Re: [Samtools-help] Calling indels with noisy reads James Bonfield
2018/05/03 Re: [Samtools-help] Calling indels with noisy reads James Bonfield
2018/05/02 Re: [Samtools-help] Calling indels with noisy reads Jody Phelan
2018/05/02 [Samtools-help] (no subject) Jody Phelan
2018/05/01 Re: [Samtools-help] Calling indels with noisy reads James Bonfield
2018/05/01 [Samtools-help] Calling indels with noisy reads Jody Phelan
2018/04/25 Re: [Samtools-help] Bug in tabix: ignores 0-based (-0) option. Heredia Genestar, Txema
2018/04/17 Re: [Samtools-help] Bug in tabix: ignores 0-based (-0) option. John Marshall
2018/04/17 Re: [Samtools-help] Bug in tabix: ignores 0-based (-0) option. Heredia Genestar, Txema
2018/04/17 Re: [Samtools-help] Bug in tabix: ignores 0-based (-0) option. Heredia Genestar, Txema
2018/04/17 Re: [Samtools-help] Bug in tabix: ignores 0-based (-0) option. John Marshall
2018/04/16 [Samtools-help] Tabix -R extracts a region given a bed file Ming Liu
2018/04/16 [Samtools-help] Bug in tabix: ignores 0-based (-0) option. Heredia Genestar, Txema
2018/04/16 Re: [Samtools-help] samtools view -L option Robert Davies
2018/04/15 [Samtools-help] samtools view -L option RITSUKO OIKAWA
2018/04/06 Re: [Samtools-help] calmd and lower case characters ernesto.picardi
2018/04/06 Re: [Samtools-help] calmd and lower case characters James Bonfield
2018/04/05 [Samtools-help] calmd and lower case characters ernesto.picardi
2018/04/03 [Samtools-help] Release 1.8 Robert Davies
2018/03/30 [Samtools-help] HELP Nurislam Shaikhutdinov
2018/03/10 Re: [Samtools-help] Extremely long reference sequences Nowoshilow,Sergej
2018/03/10 Re: [Samtools-help] Extremely long reference sequences Martin MOKREJŠ
2018/03/10 Re: [Samtools-help] Extremely long reference sequences Nowoshilow,Sergej
2018/03/10 Re: [Samtools-help] Extremely long reference sequences John Marshall
2018/03/09 Re: [Samtools-help] Extremely long reference sequences Nowoshilow,Sergej
2018/03/09 Re: [Samtools-help] Extremely long reference sequences Thomas W. Blackwell
2018/03/09 [Samtools-help] Extremely long reference sequences Nowoshilow,Sergej
2018/03/07 Re: [Samtools-help] samtools pileup format: insertions and deletions' quality James Bonfield
2018/03/06 [Samtools-help] samtools pileup format: insertions and deletions' quality Jing meng
2018/02/28 Re: [Samtools-help] REF_CACHE Brent Pedersen
2018/02/22 Re: [Samtools-help] mpileup output (base column) Nicholas Hill
2018/02/22 Re: [Samtools-help] mpileup output (base column) John Marshall
2018/02/21 Re: [Samtools-help] mpileup output (base column) Thomas W. Blackwell
2018/02/21 [Samtools-help] mpileup output (base column) Nicholas Hill
2018/02/15 [Samtools-help] question about how to use the option of --rf in samtools mpileup Jing meng
2018/02/12 [Samtools-help] BCFtools 1.7 Robert Davies
2018/02/08 Re: [Samtools-help] REF_CACHE James Bonfield
2018/02/08 [Samtools-help] REF_CACHE Brent Pedersen
2018/02/06 Re: [Samtools-help] Bcftools indel filtering Petr Danecek
2018/02/06 Re: [Samtools-help] Bcftools indel filtering James Bonfield
2018/02/06 Re: [Samtools-help] Bcftools indel filtering Petr Danecek
2018/02/05 [Samtools-help] Bcftools indel filtering James Bonfield
2018/02/01 Re: [Samtools-help] sort sam file using samtools sort Robert Davies
2018/01/31 [Samtools-help] sort sam file using samtools sort Yogesh Gupta
2018/01/26 [Samtools-help] (no subject) Robert Davies
2018/01/21 [Samtools-help] 答复: samtools view error: convert SAM to BAM fail silently (fwd) Hu Jing
2018/01/02 Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently (fwd) Robert Davies
2018/01/02 Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently Thomas W. Blackwell
2018/01/01 Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently Hu Jing
2017/12/25 Re: [Samtools-help] samtools view error: convert SAM to BAM fail silently Adrian Pelin
2017/12/25 [Samtools-help] samtools view error: convert SAM to BAM fail silently Hu Jing
2017/12/20 Re: [Samtools-help] CSI stats bins Brent Pedersen
2017/12/17 [Samtools-help] Error when installing samtools-1.6 (error: âSAMTOOLS_VERSIONâ undeclared (first use in this function) Lidia Lasecka
2017/12/14 Re: [Samtools-help] CSI stats bins John Marshall
2017/12/14 [Samtools-help] CSI stats bins Brent Pedersen
2017/12/05 [Samtools-help] Changing I16 calculation in mpileup Emily W
2017/11/30 [Samtools-help] Option -a in mpileup does not work with output option --VCF Anna Quaglieri
2017/11/30 Re: [Samtools-help] samtool installation Adam Witney
2017/11/30 Re: [Samtools-help] samtool installation James Bonfield
2017/11/30 [Samtools-help] samtool installation k.scharf
2017/11/23 Re: [Samtools-help] Samtools-help Digest, Vol 106, Issue 7 VIB | Stephane Plaisance
2017/11/21 [Samtools-help] samtools/libbam.a undefined reference Nicholas Kline
2017/11/20 Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1 Robert Davies
2017/11/20 Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1 John Marshall
2017/11/17 Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1 VIB | Stephane Plaisance
2017/11/17 Re: [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1 Robert Davies
2017/11/17 [Samtools-help] Issue Building htslib and samtools 1.6 on HighSierra OSX 10.13.1 VIB | Stephane Plaisance
2017/11/14 Re: [Samtools-help] help installing samtools Robert Davies
2017/11/13 [Samtools-help] help installing samtools Ricardo Fong Zazueta
2017/11/09 Re: [Samtools-help] samtools truncated file and Exec format error Susan Fairley
2017/11/08 Re: [Samtools-help] samtools truncated file and Exec format error Susan Fairley
2017/11/08 Re: [Samtools-help] samtools truncated file and Exec format error Robert Davies
2017/11/08 Re: [Samtools-help] samtools truncated file and Exec format error Susan Fairley
2017/11/08 Re: [Samtools-help] samtools truncated file and Exec format error John Marshall
2017/11/08 Re: [Samtools-help] samtools truncated file and Exec format error Robert Davies
2017/11/08 [Samtools-help] samtools truncated file and Exec format error Tommy Carstensen
2017/11/07 Re: [Samtools-help] crai James Bonfield
2017/11/07 [Samtools-help] crai Brent Pedersen
2017/10/31 [Samtools-help] Understanding indel format Mulini Reddy Pingili, GW/US
2017/10/02 Re: [Samtools-help] questions on "samtools mpileup count of reads" James Bonfield
2017/10/01 [Samtools-help] questions on "samtools mpileup count of reads" ????
2017/09/29 Re: [Samtools-help] csi index while bgzipping Brent Pedersen
2017/09/28 [Samtools-help] Release 1.6 Robert Davies
2017/09/21 [Samtools-help] samtools-help mailing list (tabix is part of the samtools project). ????????
2017/09/19 [Samtools-help] csi index while bgzipping Brent Pedersen
2017/09/07 [Samtools-help] Understanding the output of the samtools variant calling pipeline Niklas Mather
2017/09/04 Re: [Samtools-help] Samtools-help Digest, Vol 104, Issue 1 Stephane Plaisance | VIB |
2017/09/03 Re: [Samtools-help] use tabix with multi-chromosome file Thomas W. Blackwell
2017/09/03 [Samtools-help] use tabix with multi-chromosome file Alan Achenbach
2017/08/30 [Samtools-help] Generating a consensus sequence Juma, John
2017/08/30 Re: [Samtools-help] samtools rmdup: inconsistent bam file for paired-end reads Joseph Fass
2017/08/30 Re: [Samtools-help] hts_set_threads for n==1 James Bonfield
2017/08/30 [Samtools-help] samtools rmdup: inconsistent bam file for paired-end reads Qian Li
2017/08/30 [Samtools-help] samtools rmdup: inconsistent bam file for paired-end reads Qian Li
2017/08/29 Re: [Samtools-help] hts_set_threads for n==1 Brent Pedersen
2017/08/29 Re: [Samtools-help] hts_set_threads for n==1 James Bonfield
2017/08/28 [Samtools-help] hts_set_threads for n==1 Brent Pedersen
2017/08/22 Re: [Samtools-help] Merging VCF files with bcftools Hans Vasquez-Gross
2017/08/22 Re: [Samtools-help] Merging VCF files with bcftools Thomas W. Blackwell
2017/08/22 [Samtools-help] Merging VCF files with bcftools Hans Vasquez-Gross
2017/08/18 Re: [Samtools-help] no output when sort bam files by read names Yan Li
2017/08/18 Re: [Samtools-help] no output when sort bam files by read names John Marshall
2017/08/17 [Samtools-help] no output when sort bam files by read names Yan Li
2017/08/10 [Samtools-help] variant call difference between bcftools 1.3.1 and 1.5 Adam Witney
2017/07/12 Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites Kristian Ullrich
2017/07/12 Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites James Bonfield
2017/07/12 Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites Kristian Ullrich
2017/07/12 Re: [Samtools-help] samtools mpileup / bcftools mpileup / missing sites James Bonfield
2017/07/12 [Samtools-help] samtools mpileup / bcftools mpileup / missing sites Kristian Ullrich
2017/07/12 Re: [Samtools-help] Using Samtools as a Dependency: Getting a large amount of binary in terminal window Robert Davies
2017/07/11 [Samtools-help] Using Samtools as a Dependency: Getting a large amount of binary in terminal window Amelia Lawrence
2017/07/07 Re: [Samtools-help] additional header lines "@GA" John Marshall
2017/07/07 [Samtools-help] additional header lines "@GA" Gerben Menschaert
2017/06/25 Re: [Samtools-help] Samtools-help Digest, Vol 101, Issue 4 Stephane Plaisance
2017/06/23 [Samtools-help] Help with mpileup Maraike Probst
2017/06/21 [Samtools-help] [Samtools-devel] Release 1.5 Valeriu Ohan
2017/06/20 Re: [Samtools-help] Rare variants calling Peter Johansson
2017/06/20 Re: [Samtools-help] Rare variants calling ibseq12
2017/06/20 [Samtools-help] Rare variants calling Jody Phelan
2017/06/19 [Samtools-help] Install problems Matt Evans
2017/06/11 [Samtools-help] Ssage of samtools pileup -c -f in new version of samtools mpileup YaoXia
2017/05/22 Re: [Samtools-help] Unable to view remote bam files from 1000genomes James Bonfield
2017/05/18 [Samtools-help] Unable to view remote bam files from 1000genomes Andrew Maksymowsky
2017/05/12 Re: [Samtools-help] samtools merge issue Margres, Mark J
2017/05/12 Re: [Samtools-help] samtools merge issue Thomas W. Blackwell
2017/05/12 Re: [Samtools-help] samtools merge issue Margres, Mark J
2017/05/12 Re: [Samtools-help] samtools merge issue Thomas W. Blackwell
2017/05/12 [Samtools-help] samtools merge issue Margres, Mark J
2017/05/11 Re: [Samtools-help] crai Brent Pedersen
2017/05/11 Re: [Samtools-help] crai James Bonfield
2017/05/11 Re: [Samtools-help] crai James Bonfield
2017/05/11 Re: [Samtools-help] crai James Bonfield
2017/05/10 [Samtools-help] crai Brent Pedersen
2017/05/09 Re: [Samtools-help] Compile error htslib-1.4.1 Waldron, Michael H
2017/05/09 Re: [Samtools-help] Compile error htslib-1.4.1 James Bonfield
2017/05/08 [Samtools-help] Compile error htslib-1.4.1 Waldron, Michael H
2017/05/08 Re: [Samtools-help] Predicted het GT where hom alt expected Thomas W. Blackwell
2017/05/08 [Samtools-help] Predicted het GT where hom alt expected urs . lahrmann
2017/04/25 [Samtools-help] hts_itr_t reuse clw
2017/04/20 Re: [Samtools-help] problem with samtools mpileup kenichi chiba
2017/04/20 [Samtools-help] phased vcf from phased Bam Shilpa Garg
2017/04/20 Re: [Samtools-help] problem with samtools mpileup Federico Abascal
2017/04/20 Re: [Samtools-help] problem with samtools mpileup James Bonfield
2017/04/20 [Samtools-help] problem with samtools mpileup kenichi chiba
2017/04/19 Re: [Samtools-help] rmdup question Joseph Fass
2017/04/18 [Samtools-help] rmdup question oscar.migue...@mdc-berlin.de
2017/04/18 Re: [Samtools-help] error messages when using the fixref plugin Petr Danecek
2017/04/13 [Samtools-help] error messages when using the fixref plugin Jin, Ying
2017/04/06 Re: [Samtools-help] compile help James LaGasse
2017/04/06 Re: [Samtools-help] compile help Marcel Martin
2017/04/06 Re: [Samtools-help] compile help Peter Cock
2017/04/06 [Samtools-help] compile help James LaGasse
2017/04/06 Re: [Samtools-help] ERR: [bam_header_read] EOF marker is absent. The input is probably truncated James Bonfield
2017/04/05 [Samtools-help] ERR: [bam_header_read] EOF marker is absent. The input is probably truncated Zhiliang Hu
2017/04/04 Re: [Samtools-help] Help in calling indel Petr Danecek
2017/04/03 [Samtools-help] Help in calling indel Fox, Dylan
2017/04/01 Re: [Samtools-help] help for samtools Thomas W. Blackwell
2017/04/01 [Samtools-help] help for samtools 王玥
2017/03/24 Re: [Samtools-help] bams with malformed region names lead to variant calls using -l to be incorrect Liyang Diao
2017/03/24 Re: [Samtools-help] bams with malformed region names lead to variant calls using -l to be incorrect Shuoguo Wang
2017/03/24 Re: [Samtools-help] bams with malformed region names lead to variant calls using -l to be incorrect Thomas W. Blackwell
2017/03/23 [Samtools-help] bams with malformed region names lead to variant calls using -l to be incorrect Liyang Diao
2017/03/23 [Samtools-help] query about mpileup and bcftool calls Prasun Dutta
2017/03/17 Re: [Samtools-help] some samtools commands require sorted input - is the output guaranteed to be still in the same sort order? James Bonfield
2017/03/17 [Samtools-help] some samtools commands require sorted input - is the output guaranteed to be still in the same sort order? Anton Kratz
2017/03/08 Re: [Samtools-help] how to uninstall scar
2017/03/08 Re: [Samtools-help] how to uninstall Sven Klages
2017/03/08 Re: [Samtools-help] how to uninstall Colin
2017/03/08 Re: [Samtools-help] bgzip file index and fasta file sebastien letort
2017/03/08 Re: [Samtools-help] bgzip file index and fasta file Colin
2017/03/07 [Samtools-help] bgzip file index and fasta file sebastien letort
2017/03/06 Re: [Samtools-help] Problem Converting BAM to SAM on to Amazon-S3 Using Samtools scar
2017/03/06 Re: [Samtools-help] help for " samtools tview -d" scar
2017/03/06 [Samtools-help] how to uninstall scar
2017/03/06 [Samtools-help] bgzip file index and fasta file sebastien letort
2017/03/05 Re: [Samtools-help] read alignment number limitation shown in samtools tview huyudong
2017/03/04 Re: [Samtools-help] read alignment number limitation shown in samtools tview Dario Beraldi
2017/03/03 Re: [Samtools-help] Is there a way how I can figure out how many reads have been removed by applying rmdup? Christian Cole (Staff)
2017/03/03 [Samtools-help] read alignment number limitation shown in samtools tview huyudong
2017/03/02 Re: [Samtools-help] BCF2.2 and VCF version interop Petr Danecek
2017/03/02 [Samtools-help] Is there a way how I can figure out how many reads have been removed by applying rmdup? Anton Kratz
2017/02/27 [Samtools-help] BCF2.2 and VCF version interop Chris Norman
2017/02/24 [Samtools-help] Samtols paired call variant jarod...@libero.it
2017/02/22 [Samtools-help] Problem Converting BAM to SAM on to Amazon-S3 Using Samtools Gundala Viswanath
2017/02/21 Re: [Samtools-help] "Strand bias" in mutation calling with samtools-bcftools Petr Danecek