samtools-help

Messages by Date

2015/11/13 [Samtools-help] Reading Custom Index - Creates many threads? Terry Casstevens
2015/11/12 [Samtools-help] Cygwin installation of SamTools Christopher Wozniak
2015/11/11 Re: [Samtools-help] Installation problems on Windows Karel Břinda
2015/11/11 [Samtools-help] Installation problems on Windows Christopher Wozniak
2015/11/08 [Samtools-help] pileup format ?? Norge Cruz Hernández
2015/11/06 Re: [Samtools-help] [Samtools-devel] bgzip performance? Nils Homer
2015/11/06 [Samtools-help] bgzip performance? Terry Casstevens
2015/11/06 Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
2015/11/06 Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
2015/11/06 Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
2015/11/06 Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
2015/11/06 Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
2015/11/05 Re: [Samtools-help] samtools index commands pretends it has succeeded, but it has not Michael Nuhn
2015/11/05 Re: [Samtools-help] samtools index commands pretends it has succeeded, but it has not John Marshall
2015/11/05 [Samtools-help] samtools index commands pretends it has succeeded, but it has not Michael Nuhn
2015/11/05 Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
2015/11/05 Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
2015/11/05 Re: [Samtools-help] bcftools annotate could not parse header line John Marshall
2015/11/04 [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
2015/11/03 Re: [Samtools-help] A question from Fang Liang Thomas W. Blackwell
2015/11/02 [Samtools-help] A question from Fang Liang 梁芳
2015/10/29 [Samtools-help] mpileup multisample Flavia Palombo
2015/10/27 [Samtools-help] merging indexes Ogan Abaan
2015/10/27 Re: [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file James Bonfield
2015/10/27 Re: [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file Devon Ryan
2015/10/27 [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file imamovic
2015/10/26 Re: [Samtools-help] change cigar value in the source code for a bam file. James Bonfield
2015/10/23 [Samtools-help] change cigar value in the source code for a bam file. Bingding Huang
2015/10/17 Re: [Samtools-help] HTSJDK - Depth of Coverage function? Dario Beraldi
2015/10/16 [Samtools-help] HTSJDK - Depth of Coverage function? Chad S Harland
2015/10/12 Re: [Samtools-help] samtools error: [E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1 David K Jackson
2015/10/09 [Samtools-help] samtools indexing bam jeremy le luyer
2015/10/08 [Samtools-help] SAM to BAM error :[main_samview] truncated file. 刘放 Fang Liu
2015/10/07 [Samtools-help] samtools error: [E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1 Sandeep Marla
2015/10/06 [Samtools-help] Bug in DP4 calculation for indels Christian Ruckert
2015/10/05 Re: [Samtools-help] bgzip removal of EOF blocks? Pär Larsson
2015/10/05 Re: [Samtools-help] bgzip removal of EOF blocks? John Marshall
2015/10/03 [Samtools-help] bgzip removal of EOF blocks? Pär Larsson
2015/09/28 Re: [Samtools-help] Samtools faidx "Segmentation fault (core dumped)" John Marshall
2015/09/28 [Samtools-help] Samtools faidx "Segmentation fault (core dumped)" Maria Sutton
2015/09/25 [Samtools-help] Merge and fixmate of multiple BAM files generated from pair-end DNA sequences Lisa Davis
2015/09/22 [Samtools-help] htsjdk (convert / validate bgzip file) Terry Casstevens
2015/09/21 Re: [Samtools-help] Samtools mpileup: some positions missing fields John Marshall
2015/09/17 Re: [Samtools-help] BG Zip Terry Casstevens
2015/09/16 [Samtools-help] Samtools mpileup: some positions missing fields Brendan Kohrn
2015/09/11 [Samtools-help] Samtools mpileup reference error matteo di giovannantonio
2015/09/11 [Samtools-help] Samtools fails to open the h19.fasta file downloaded from the GATK resource bundle FTP. How to fix the problem? Thanks a lot! lcai
2015/09/11 Re: [Samtools-help] BG Zip John Marshall
2015/09/11 Re: [Samtools-help] BG Zip Peter Cock
2015/09/10 [Samtools-help] BG Zip Terry Casstevens
2015/09/10 Re: [Samtools-help] Unable to create .fai and use mpileup Thomas W. Blackwell
2015/09/10 [Samtools-help] Unable to create .fai and use mpileup Manuel Riveros
2015/09/10 [Samtools-help] Homopolymer-Problem using mpileup Sarah Sandmann
2015/09/08 [Samtools-help] Interpretation of SM and LB tags of @RG headers for multiplexed sequencing Bob Handsaker
2015/09/08 [Samtools-help] bcftools-stats on more than 2 files James Blackshaw
2015/09/07 Re: [Samtools-help] Pileup format John Marshall
2015/09/07 [Samtools-help] Pileup format Tom Adlerteg
2015/09/02 [Samtools-help] samtools 1.2 may have a bug regarding option �Cskip-indels Ma, Qicheng
2015/09/01 [Samtools-help] how to generate mpileup output for indels similar to pileup output for indels Ma, Qicheng
2015/08/28 [Samtools-help] Problem with tabix indexing Diego Diaz Dominguez
2015/08/28 [Samtools-help] Error when using plot-vcfstats on multiple stats files James Blackshaw
2015/08/28 [Samtools-help] bcftools sort -c Joao Dias
2015/08/27 [Samtools-help] Current mpileup BAQ recommendations Christian Ruckert
2015/08/27 [Samtools-help] Differences between IDV and DP4 Christian Ruckert
2015/08/27 Re: [Samtools-help] what is a reference skip? John Marshall
2015/08/27 [Samtools-help] what is a reference skip? Samantha Klasfeld
2015/08/26 Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
2015/08/26 Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup Thomas W. Blackwell
2015/08/26 Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
2015/08/24 Re: [Samtools-help] indels in mpileup Jo R
2015/08/24 [Samtools-help] The flag problem in Markduplicates Hong Zhang
2015/08/24 [Samtools-help] TabixReader Terry Casstevens
2015/08/22 [Samtools-help] indels in mpileup Jo R
2015/08/21 Re: [Samtools-help] CRAM index files Vadim Zalunin
2015/08/21 Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
2015/08/20 Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup Thomas W. Blackwell
2015/08/20 Re: [Samtools-help] samtools sort Colin Hercus
2015/08/20 Re: [Samtools-help] samtools sort Peter Cock
2015/08/20 Re: [Samtools-help] samtools sort Peter Cock
2015/08/20 Re: [Samtools-help] samtools sort Joao Dias
2015/08/20 [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
2015/08/18 [Samtools-help] How do I interpret the output of bcftools stats? James Blackshaw
2015/08/18 Re: [Samtools-help] CRAM index files James Bonfield
2015/08/17 [Samtools-help] multi alleleic SNPs Henke, Katrin
2015/08/17 Re: [Samtools-help] CRAM index files Vadim Zalunin
2015/08/17 Re: [Samtools-help] CRAM index files James Bonfield
2015/08/17 Re: [Samtools-help] CRAM index files James Bonfield
2015/08/17 Re: [Samtools-help] samtools idxstats on cram James Bonfield
2015/08/14 [Samtools-help] samtools idxstats on cram Holly Zheng Bradley
2015/08/13 [Samtools-help] Inconsistent results from SamReader/SamLocusIterator on Ubuntu 14 but not Ubuntu 12 Phil Shapiro
2015/08/12 Re: [Samtools-help] CRAM index files jkb
2015/08/12 Re: [Samtools-help] CRAM index files David Roazen
2015/08/12 Re: [Samtools-help] CRAM index files jkb
2015/08/12 [Samtools-help] samtools sort Joao Dias
2015/08/11 [Samtools-help] A question about QS value from vcf format Teeratas Kijpornyongpan
2015/08/11 Re: [Samtools-help] removing references w/o any alignments from the header Devon Ryan
2015/08/11 [Samtools-help] removing references w/o any alignments from the header Bala Ani Akpinar
2015/08/11 [Samtools-help] Hi~~ I have questions. 최윤영
2015/08/07 [Samtools-help] samtools help me 전준범
2015/08/07 [Samtools-help] CRAM index files Edward Kwiatkowski
2015/08/06 [Samtools-help] A question about QS value from vcf format Teeratas Kijpornyongpan
2015/08/05 Re: [Samtools-help] about samtools view -L Hongdong Li
2015/08/04 Re: [Samtools-help] about samtools view -L Heng Li
2015/07/31 [Samtools-help] Novel allele QV Iria Roca
2015/07/27 [Samtools-help] mpileup error(?) 성동은
2015/07/27 Re: [Samtools-help] samtools sort removes @RG header line, but leaves RG tags in alignments John Marshall
2015/07/27 [Samtools-help] samtools sort removes @RG header line, but leaves RG tags in alignments Patrick Reilly
2015/07/27 Re: [Samtools-help] samtools index error [E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 Thomas W. Blackwell
2015/07/27 Re: [Samtools-help] samtools index error [E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 Thomas W. Blackwell
2015/07/27 [Samtools-help] samtools index error [E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 Komal Rathi
2015/07/23 [Samtools-help] Confusion of samtools mpileup output format pepsisee
2015/07/15 [Samtools-help] Question about sam to bam convertion 雷鸣
2015/07/13 Re: [Samtools-help] mpileup -l BED region file 0-based problem Guillermo Marco Puche
2015/07/13 [Samtools-help] mpileup -l BED region file 0-based problem Guillermo Marco Puche
2015/07/10 [Samtools-help] Multiple Variants Min Seong Kim
2015/07/09 Re: [Samtools-help] gtcheck functionality Petr Danecek
2015/07/08 Re: [Samtools-help] bcftools merge broken record Petr Danecek
2015/07/08 Re: [Samtools-help] bcftools synced_bcf_reader error Petr Danecek
2015/07/08 Re: [Samtools-help] Big Data: Astronomical or Genomical? Fengyuan Hu
2015/07/08 [Samtools-help] Big Data: Astronomical or Genomical? Fengyuan Hu
2015/07/07 Re: [Samtools-help] Header Joshua Bradley
2015/07/07 Re: [Samtools-help] Header ma . meyerheim
2015/07/06 Re: [Samtools-help] Header John Marshall
2015/07/06 Re: [Samtools-help] Header Joshua Bradley
2015/07/06 Re: [Samtools-help] Header ma . meyerheim
2015/07/06 Re: [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time James Bonfield
2015/07/06 Re: [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time Peter Cock
2015/07/06 [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time Albert Vilella
2015/07/06 [Samtools-help] BAQ on RNA-seq variant calling Manuel Landesfeind
2015/07/03 Re: [Samtools-help] bcftools merge broken record Sébastien Letort
2015/07/03 [Samtools-help] gtcheck functionality Arti Tandon
2015/07/03 Re: [Samtools-help] bcftools merge broken record Thomas W. Blackwell
2015/07/03 [Samtools-help] bcftools merge broken record Sébastien Letort
2015/07/02 [Samtools-help] bcftools synced_bcf_reader error Kerry Deutsch
2015/07/02 Re: [Samtools-help] Header Joshua Bradley
2015/07/02 [Samtools-help] Header ma . meyerheim
2015/07/01 Re: [Samtools-help] Choosing CRAM Format to Output James Bonfield
2015/07/01 Re: [Samtools-help] Choosing CRAM Format to Output Jeffrey Tratner
2015/07/01 Re: [Samtools-help] Choosing CRAM Format to Output James Bonfield
2015/07/01 [Samtools-help] Choosing CRAM Format to Output Jeffrey Tratner
2015/06/29 [Samtools-help] why my vcf file qual column are decimals lkp123
2015/06/26 Re: [Samtools-help] CollectOxoGMetrics Nils Homer
2015/06/24 [Samtools-help] CollectOxoGMetrics laillern
2015/06/23 [Samtools-help] Picard CollectRnaSeqMetrics George Greene
2015/06/22 Re: [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Noa Henig
2015/06/22 Re: [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Nils Homer
2015/06/21 [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Noa Henig
2015/06/19 [Samtools-help] CollectGbBiasMetrics Error Rebecca Panitch
2015/06/19 [Samtools-help] Help remove contaminants david martin
2015/06/19 [Samtools-help] changelog picard Maarten Kooyman
2015/06/17 [Samtools-help] different BED, same position, different INDEL? 郭阳
2015/06/16 Re: [Samtools-help] samtools merge Lo, Chien-Chi
2015/06/16 Re: [Samtools-help] samtools merge John Marshall
2015/06/16 Re: [Samtools-help] samtools merge James Bonfield
2015/06/15 [Samtools-help] help with -q option in mpileup E. Warwick Daw
2015/06/15 Re: [Samtools-help] samtools merge Lo, Chien-Chi
2015/06/15 [Samtools-help] bgzip and tabix Ayshin Gahalichi
2015/06/12 Re: [Samtools-help] Samtools documentation typo Petr Danecek
2015/06/11 [Samtools-help] Samtools documentation typo Joshua Bradley
2015/06/11 Re: [Samtools-help] wrong output format of bwa? Hansen, Nancy (NIH/NHGRI) [E]
2015/06/11 Re: [Samtools-help] wrong output format of bwa? Thomas W. Blackwell
2015/06/10 [Samtools-help] wrong output format of bwa? 刘放 Fang Liu
2015/06/10 [Samtools-help] Missing DP for bcftools gtcheck Ogan
2015/06/05 [Samtools-help] mpileup QUAL column all zeros dm
2015/06/04 [Samtools-help] rmdup algorithm Mark Wadsworth
2015/06/03 Re: [Samtools-help] Samtools and Custom Read annotation Piet Jones
2015/06/03 Re: [Samtools-help] Samtools and Custom Read annotation Heng Li
2015/06/03 [Samtools-help] Samtools and Custom Read annotation Piet Jones
2015/05/29 Re: [Samtools-help] how to chose SAM flags Dario Copetti
2015/05/29 Re: [Samtools-help] how to chose SAM flags James Bonfield
2015/05/28 [Samtools-help] how to chose SAM flags Dario Copetti
2015/05/27 [Samtools-help] I'm trying to sort a vcf by reference dict Jean-Philippe Villemin
2015/05/26 Re: [Samtools-help] how to convert fasta to bam format Christian Cole (Staff)
2015/05/26 Re: [Samtools-help] Help using samtools to get fastq from sorted bam Devon Ryan
2015/05/26 [Samtools-help] Help using samtools to get fastq from sorted bam Wei Quan Low
2015/05/22 Re: [Samtools-help] how to convert fasta to bam format Vanessa Oliveira
2015/05/22 Re: [Samtools-help] how to convert fasta to bam format Peter Cock
2015/05/21 [Samtools-help] mpileup on GrCH38 not showing strand info Rebecca Halperin
2015/05/21 [Samtools-help] how to convert fasta to bam format Vanessa Oliveira
2015/05/21 Re: [Samtools-help] Licencing Question James Bonfield
2015/05/21 Re: [Samtools-help] Licencing Question Peter Cock
2015/05/21 [Samtools-help] Licencing Question Daniel Reynolds (CMP)
2015/05/19 Re: [Samtools-help] some help on using htslib Zhihao Ding
2015/05/19 [Samtools-help] CalculateHsMetrics error Mónica Fabbro
2015/05/19 Re: [Samtools-help] some help on using htslib Petr Danecek
2015/05/19 [Samtools-help] (no subject) Mónica Fabbro
2015/05/19 Re: [Samtools-help] [E::hts_hopen] samtools index problem Christian Cole (Staff)
2015/05/19 Re: [Samtools-help] Fwd: tabix interval at deletion sites Petr Danecek
2015/05/19 Re: [Samtools-help] Fwd: tabix interval at deletion sites Hannes Svardal
2015/05/19 Re: [Samtools-help] Fwd: tabix interval at deletion sites Petr Danecek
2015/05/19 Re: [Samtools-help] some help on using htslib Petr Danecek
2015/05/19 [Samtools-help] some help on using htslib Zhihao Ding
2015/05/19 Re: [Samtools-help] [E::hts_hopen] samtools index problem Christian Cole (Staff)
2015/05/19 Re: [Samtools-help] mpileup discrepancy Samtools 0.1.19 and 1.2 for depth values Dessislava Mladenova
2015/05/19 [Samtools-help] [E::hts_hopen] samtools index problem Siva Nandy
2015/05/18 [Samtools-help] mpileup discrepancy Samtools 0.1.19 and 1.2 for depth values Dessislava Mladenova
2015/05/18 [Samtools-help] Fwd: tabix interval at deletion sites Hannes Svardal
2015/05/18 Re: [Samtools-help] Failed BAM -> CRAM -> BAM James Bonfield
2015/05/18 Re: [Samtools-help] Failed BAM -> CRAM -> BAM James Bonfield
2015/05/18 Re: [Samtools-help] Failed BAM -> CRAM -> BAM Sendu Bala