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• [Samtools-help] samtools index commands pretends it has succeeded, but it has not Michael Nuhn
  • Re: [Samtools-help] samtools index commands pretends it has succeeded, but it has not John Marshall
  • Re: [Samtools-help] samtools index commands pretends it has succeeded, but it has not Michael Nuhn
• [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
  • Re: [Samtools-help] bcftools annotate could not parse header line John Marshall
  • Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
  • Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
  • Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
  • Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
  • Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
  • Re: [Samtools-help] bcftools annotate could not parse header line Petr Danecek
  • Re: [Samtools-help] bcftools annotate could not parse header line Tagliamonte,Massimiliano S
• [Samtools-help] A question from Fang Liang 梁芳
  • Re: [Samtools-help] A question from Fang Liang Thomas W. Blackwell
• [Samtools-help] mpileup multisample Flavia Palombo
• [Samtools-help] merging indexes Ogan Abaan
• [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file imamovic
  • Re: [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file Devon Ryan
  • Re: [Samtools-help] Extracting aligned reads from a bam file from regions specified in a .bed file James Bonfield
• [Samtools-help] change cigar value in the source code for a bam file. Bingding Huang
  • Re: [Samtools-help] change cigar value in the source code for a bam file. James Bonfield
• [Samtools-help] HTSJDK - Depth of Coverage function? Chad S Harland
  • Re: [Samtools-help] HTSJDK - Depth of Coverage function? Dario Beraldi
• [Samtools-help] samtools indexing bam jeremy le luyer
• [Samtools-help] SAM to BAM error :[main_samview] truncated file. 刘放 Fang Liu
• [Samtools-help] samtools error: [E::hts_idx_push] NO_COOR reads not in a single block at the end 2 -1 Sandeep Marla
  • 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
• [Samtools-help] Bug in DP4 calculation for indels Christian Ruckert
• [Samtools-help] bgzip removal of EOF blocks? Pär Larsson
  • Re: [Samtools-help] bgzip removal of EOF blocks? John Marshall
  • Re: [Samtools-help] bgzip removal of EOF blocks? Pär Larsson
• [Samtools-help] Samtools faidx "Segmentation fault (core dumped)" Maria Sutton
  • Re: [Samtools-help] Samtools faidx "Segmentation fault (core dumped)" John Marshall
• [Samtools-help] Merge and fixmate of multiple BAM files generated from pair-end DNA sequences Lisa Davis
• [Samtools-help] htsjdk (convert / validate bgzip file) Terry Casstevens
• [Samtools-help] Samtools mpileup: some positions missing fields Brendan Kohrn
  • Re: [Samtools-help] Samtools mpileup: some positions missing fields John Marshall
• [Samtools-help] Samtools mpileup reference error matteo di giovannantonio
• [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
• [Samtools-help] BG Zip Terry Casstevens
  • Re: [Samtools-help] BG Zip Peter Cock
  • Re: [Samtools-help] BG Zip John Marshall
  • Re: [Samtools-help] BG Zip Terry Casstevens
• [Samtools-help] Unable to create .fai and use mpileup Manuel Riveros
  • Re: [Samtools-help] Unable to create .fai and use mpileup Thomas W. Blackwell
• [Samtools-help] Homopolymer-Problem using mpileup Sarah Sandmann
• [Samtools-help] Interpretation of SM and LB tags of @RG headers for multiplexed sequencing Bob Handsaker
• [Samtools-help] bcftools-stats on more than 2 files James Blackshaw
• [Samtools-help] Pileup format Tom Adlerteg
  • Re: [Samtools-help] Pileup format John Marshall
• [Samtools-help] samtools 1.2 may have a bug regarding option �Cskip-indels Ma, Qicheng
• [Samtools-help] how to generate mpileup output for indels similar to pileup output for indels Ma, Qicheng
• [Samtools-help] Problem with tabix indexing Diego Diaz Dominguez
• [Samtools-help] Error when using plot-vcfstats on multiple stats files James Blackshaw
• [Samtools-help] bcftools sort -c Joao Dias
• [Samtools-help] Current mpileup BAQ recommendations Christian Ruckert
• [Samtools-help] Differences between IDV and DP4 Christian Ruckert
• [Samtools-help] what is a reference skip? Samantha Klasfeld
  • Re: [Samtools-help] what is a reference skip? John Marshall
• [Samtools-help] The flag problem in Markduplicates Hong Zhang
• [Samtools-help] TabixReader Terry Casstevens
• [Samtools-help] indels in mpileup Jo R
  • Re: [Samtools-help] indels in mpileup Jo R
• [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
  • Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup Thomas W. Blackwell
  • Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
  • Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
  • Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup Thomas W. Blackwell
  • Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup 梁芳
• [Samtools-help] How do I interpret the output of bcftools stats? James Blackshaw
• [Samtools-help] multi alleleic SNPs Henke, Katrin
• [Samtools-help] samtools idxstats on cram Holly Zheng Bradley
  • Re: [Samtools-help] samtools idxstats on cram James Bonfield
• [Samtools-help] Inconsistent results from SamReader/SamLocusIterator on Ubuntu 14 but not Ubuntu 12 Phil Shapiro
• [Samtools-help] removing references w/o any alignments from the header Bala Ani Akpinar
  • Re: [Samtools-help] removing references w/o any alignments from the header Devon Ryan
• [Samtools-help] Hi~~ I have questions. 최윤영
• [Samtools-help] samtools help me 전준범
• [Samtools-help] CRAM index files Edward Kwiatkowski
  • Re: [Samtools-help] CRAM index files jkb
  • Re: [Samtools-help] CRAM index files David Roazen
  • Re: [Samtools-help] CRAM index files jkb
  • Re: [Samtools-help] CRAM index files James Bonfield
  • Re: [Samtools-help] CRAM index files James Bonfield
  • Re: [Samtools-help] CRAM index files Vadim Zalunin
  • Re: [Samtools-help] CRAM index files James Bonfield
  • Re: [Samtools-help] CRAM index files Vadim Zalunin
• [Samtools-help] A question about QS value from vcf format Teeratas Kijpornyongpan
  • [Samtools-help] A question about QS value from vcf format Teeratas Kijpornyongpan
• Re: [Samtools-help] about samtools view -L Heng Li
  • Re: [Samtools-help] about samtools view -L Hongdong Li
• [Samtools-help] Novel allele QV Iria Roca
• [Samtools-help] mpileup error(?) 성동은
• [Samtools-help] samtools sort removes @RG header line, but leaves RG tags in alignments Patrick Reilly
  • Re: [Samtools-help] samtools sort removes @RG header line, but leaves RG tags in alignments John Marshall
• [Samtools-help] samtools index error [E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 Komal Rathi
  • 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
  • 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
• [Samtools-help] Confusion of samtools mpileup output format pepsisee
• [Samtools-help] Question about sam to bam convertion 雷鸣
• [Samtools-help] mpileup -l BED region file 0-based problem Guillermo Marco Puche
  • Re: [Samtools-help] mpileup -l BED region file 0-based problem Guillermo Marco Puche
• [Samtools-help] Multiple Variants Min Seong Kim
• [Samtools-help] Big Data: Astronomical or Genomical? Fengyuan Hu
  • Re: [Samtools-help] Big Data: Astronomical or Genomical? Fengyuan Hu
• [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time Albert Vilella
  • Re: [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time Peter Cock
  • Re: [Samtools-help] Reporting on samtools-0.1.18 sort producing a huge file and taking a long time James Bonfield
• [Samtools-help] BAQ on RNA-seq variant calling Manuel Landesfeind
• [Samtools-help] gtcheck functionality Arti Tandon
  • Re: [Samtools-help] gtcheck functionality Petr Danecek
• [Samtools-help] bcftools merge broken record Sébastien Letort
  • Re: [Samtools-help] bcftools merge broken record Thomas W. Blackwell
  • Re: [Samtools-help] bcftools merge broken record Sébastien Letort
  • Re: [Samtools-help] bcftools merge broken record Petr Danecek
• [Samtools-help] bcftools synced_bcf_reader error Kerry Deutsch
  • Re: [Samtools-help] bcftools synced_bcf_reader error Petr Danecek
• [Samtools-help] Header ma . meyerheim
  • Re: [Samtools-help] Header Joshua Bradley
  • Re: [Samtools-help] Header ma . meyerheim
  • Re: [Samtools-help] Header Joshua Bradley
  • Re: [Samtools-help] Header John Marshall
  • Re: [Samtools-help] Header ma . meyerheim
  • Re: [Samtools-help] Header Joshua Bradley
• [Samtools-help] Choosing CRAM Format to Output Jeffrey Tratner
  • Re: [Samtools-help] Choosing CRAM Format to Output James Bonfield
  • Re: [Samtools-help] Choosing CRAM Format to Output Jeffrey Tratner
  • Re: [Samtools-help] Choosing CRAM Format to Output James Bonfield
• [Samtools-help] why my vcf file qual column are decimals lkp123
• [Samtools-help] CollectOxoGMetrics laillern
  • Re: [Samtools-help] CollectOxoGMetrics Nils Homer
• [Samtools-help] Picard CollectRnaSeqMetrics George Greene
• [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Noa Henig
  • Re: [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Nils Homer
  • Re: [Samtools-help] "OutOfMemoryError: Java heap space" exception in Picard CollectMultipleMetrics Noa Henig
• [Samtools-help] CollectGbBiasMetrics Error Rebecca Panitch
• [Samtools-help] Help remove contaminants david martin
• [Samtools-help] changelog picard Maarten Kooyman
• [Samtools-help] different BED, same position, different INDEL? 郭阳
• [Samtools-help] help with -q option in mpileup E. Warwick Daw
• [Samtools-help] bgzip and tabix Ayshin Gahalichi
• [Samtools-help] Samtools documentation typo Joshua Bradley
  • Re: [Samtools-help] Samtools documentation typo Petr Danecek
• [Samtools-help] wrong output format of bwa? 刘放 Fang Liu
  • Re: [Samtools-help] wrong output format of bwa? Thomas W. Blackwell
  • Re: [Samtools-help] wrong output format of bwa? Hansen, Nancy (NIH/NHGRI) [E]
• [Samtools-help] Missing DP for bcftools gtcheck Ogan
• [Samtools-help] mpileup QUAL column all zeros dm
• [Samtools-help] rmdup algorithm Mark Wadsworth
• [Samtools-help] Samtools and Custom Read annotation Piet Jones
  • Re: [Samtools-help] Samtools and Custom Read annotation Heng Li
  • Re: [Samtools-help] Samtools and Custom Read annotation Piet Jones
• [Samtools-help] how to chose SAM flags Dario Copetti
  • Re: [Samtools-help] how to chose SAM flags James Bonfield
  • Re: [Samtools-help] how to chose SAM flags Dario Copetti
• [Samtools-help] I'm trying to sort a vcf by reference dict Jean-Philippe Villemin
• [Samtools-help] Help using samtools to get fastq from sorted bam Wei Quan Low
  • Re: [Samtools-help] Help using samtools to get fastq from sorted bam Devon Ryan
• [Samtools-help] mpileup on GrCH38 not showing strand info Rebecca Halperin
• [Samtools-help] how to convert fasta to bam format Vanessa Oliveira
  • Re: [Samtools-help] how to convert fasta to bam format Peter Cock
  • Re: [Samtools-help] how to convert fasta to bam format Vanessa Oliveira
  • Re: [Samtools-help] how to convert fasta to bam format Christian Cole (Staff)
• [Samtools-help] Licencing Question Daniel Reynolds (CMP)
  • Re: [Samtools-help] Licencing Question Peter Cock
  • Re: [Samtools-help] Licencing Question James Bonfield
• [Samtools-help] CalculateHsMetrics error Mónica Fabbro
• [Samtools-help] some help on using htslib Zhihao Ding
  • Re: [Samtools-help] some help on using htslib Petr Danecek
  • Re: [Samtools-help] some help on using htslib Petr Danecek
  • Re: [Samtools-help] some help on using htslib Zhihao Ding
• [Samtools-help] [E::hts_hopen] samtools index problem Siva Nandy
  • Re: [Samtools-help] [E::hts_hopen] samtools index problem Christian Cole (Staff)
  • Re: [Samtools-help] [E::hts_hopen] samtools index problem Christian Cole (Staff)
• [Samtools-help] mpileup discrepancy Samtools 0.1.19 and 1.2 for depth values Dessislava Mladenova
  • Re: [Samtools-help] mpileup discrepancy Samtools 0.1.19 and 1.2 for depth values Dessislava Mladenova
• [Samtools-help] Fwd: tabix interval at deletion sites Hannes Svardal
  • Re: [Samtools-help] Fwd: tabix interval at deletion sites Petr Danecek
  • Re: [Samtools-help] Fwd: tabix interval at deletion sites Hannes Svardal
  • Re: [Samtools-help] Fwd: tabix interval at deletion sites Petr Danecek
• [Samtools-help] Failed BAM -> CRAM -> BAM Dan Greenfield
  • Re: [Samtools-help] Failed BAM -> CRAM -> BAM Thomas W. Blackwell
  • Re: [Samtools-help] Failed BAM -> CRAM -> BAM Dan Greenfield
  • Re: [Samtools-help] Failed BAM -> CRAM -> BAM James Bonfield
  • Re: [Samtools-help] Failed BAM -> CRAM -> BAM Sendu Bala
  • Re: [Samtools-help] Failed BAM -> CRAM -> BAM James Bonfield
• [Samtools-help] Samtools 0.1.19 RPB value help Dessislava Mladenova
• [Samtools-help] inconsistent output vcf with sample number JINGJING JIN
• [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz Peter Cock
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz Len Trigg
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz John Marshall
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz Heng Li
  • Re: [Samtools-help] tabix bug on cat'ed vcf.gz John Marshall
• [Samtools-help] mpileup: tradeoff between runtime and accuracy Christian Ruckert
• [Samtools-help] removing bad quality reads William Gilks
• [Samtools-help] Install Picard-1.131 without internet Zhihua Li
• [Samtools-help] mpileup: different number of bases and read positions when using --output-BP Carey, Lucas

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