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• • Re: [Samtools-help] "Strand bias" in mutation calling with samtools-bcftools Jiri Nehyba
  • Re: [Samtools-help] "Strand bias" in mutation calling with samtools-bcftools Petr Danecek
• [Samtools-help] help for " samtools tview -d" 王灿
  • Re: [Samtools-help] help for " samtools tview -d" scar
• [Samtools-help] samtools fastq - is it broken? Keiran Raine
  • Re: [Samtools-help] samtools fastq - is it broken? Keiran Raine
• [Samtools-help] Getting nucleotide information from mpileup output Özcan Esen
• [Samtools-help] samtools rmdup help Qian Li
  • Re: [Samtools-help] samtools rmdup help James Bonfield
  • Re: [Samtools-help] samtools rmdup help Qian Li
• [Samtools-help] samtools mpileup help Pramod b.m
• [Samtools-help] rmdup options Elle
• [Samtools-help] Zero Length Reads in SAM Colin Hercus
  • Re: [Samtools-help] Zero Length Reads in SAM Robert Davies
  • Re: [Samtools-help] Zero Length Reads in SAM Colin Hercus
  • Re: [Samtools-help] Zero Length Reads in SAM James Bonfield
  • Re: [Samtools-help] Zero Length Reads in SAM Colin Hercus
• [Samtools-help] indexing huge BAM file Irena Fischer-Hwang
  • Re: [Samtools-help] indexing huge BAM file Tommy Carstensen
  • Re: [Samtools-help] indexing huge BAM file Thomas W. Blackwell
  • Re: [Samtools-help] indexing huge BAM file Peter Cock
  • Re: [Samtools-help] indexing huge BAM file Irena Fischer-Hwang
  • Re: [Samtools-help] indexing huge BAM file James Bonfield
• [Samtools-help] Samtools view -m James Bonfield
  • Re: [Samtools-help] [Samtools-devel] Samtools view -m Devon Ryan
• [Samtools-help] samtools stats error Madolyn Macdonald
  • Re: [Samtools-help] samtools stats error Sam Nicholls
  • Re: [Samtools-help] samtools stats error John Marshall
  • Re: [Samtools-help] samtools stats error Madolyn Macdonald
• [Samtools-help] Question regarding bam compression after sorting Angela Zou
  • Re: [Samtools-help] Question regarding bam compression after sorting James Bonfield
• [Samtools-help] please remove my email from the list Hadas Ner Gaon
  • Re: [Samtools-help] please remove my email from the list John Marshall
• [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Holbrook J .
  • [Samtools-help] FW: samtools sort for paired-end .bam cannot find chromosome name in text header Holbrook J .
  • Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Robert Davies
  • Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header John Marshall
  • Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Robert Davies
  • Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Holbrook J .
  • Re: [Samtools-help] samtools sort for paired-end .bam cannot find chromosome name in text header Holbrook J .
• Re: [Samtools-help] Samtools depth question Fauni, Harper (NIH/NHGRI) [F]
  • [Samtools-help] Samtools depth question Fauni, Harper (NIH/NHGRI) [F]
• [Samtools-help] why "samtools view" change the bam file Michael Peng
  • Re: [Samtools-help] why "samtools view" change the bam file Thomas W. Blackwell
  • Re: [Samtools-help] why "samtools view" change the bam file Michael Peng
• [Samtools-help] Samtools mpileup reference is different from input reference fasta Jacob Ulirsch
  • Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta John Marshall
  • Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta John Marshall
  • Re: [Samtools-help] Samtools mpileup reference is different from input reference fasta Jacob Ulirsch
• [Samtools-help] Information about the algorithm Sebastian Gregoricchio
  • Re: [Samtools-help] Information about the algorithm Peter Cock
  • Re: [Samtools-help] Information about the algorithm John Marshall
• [Samtools-help] bcftools merge automatically Left-align? 3110101054
• [Samtools-help] Limit number of bam files Samtools1.3 hans . daetwyler
  • Re: [Samtools-help] Limit number of bam files Samtools1.3 James Bonfield
  • Re: [Samtools-help] Limit number of bam files Samtools1.3 hans . daetwyler
  • Re: [Samtools-help] Limit number of bam files Samtools1.3 Martin MOKREJŠ
• [Samtools-help] Depth 0 though the region is covered! Qiongxian Lu
• [Samtools-help] samtools-1.2 install problem yincl2013
  • Re: [Samtools-help] samtools-1.2 install problem John Marshall
• [Samtools-help] Error when using tview Shannon Joslin
• Re: [Samtools-help] bcftools merge : multiple rows per position Davis, Steven
  • Re: [Samtools-help] bcftools merge : multiple rows per position Thomas W. Blackwell
  • Re: [Samtools-help] bcftools merge : multiple rows per position Davis, Steven
• [Samtools-help] faidx error_could not build fai index 陈然
  • Re: [Samtools-help] faidx error_could not build fai index John Marshall
  • Re: [Samtools-help] faidx error_could not build fai index John Marshall
• [Samtools-help] bcftools merge multiple rows per position Davis, Steven
• [Samtools-help] Indels, DP and DP4 Florian Battke
• [Samtools-help] HELP - converting var.flt.vcf files Rumpf, Wolfgang
  • Re: [Samtools-help] HELP - converting var.flt.vcf files Thomas W. Blackwell
  • Re: [Samtools-help] HELP - converting var.flt.vcf files James Robinson
  • Re: [Samtools-help] HELP - converting var.flt.vcf files James Robinson
• [Samtools-help] Cram conversion error: [main_samview] failed to write the SAM header Veronica Suaste Morales
  • Re: [Samtools-help] Cram conversion error: [main_samview] failed to write the SAM header Shane McCarthy
  • Re: [Samtools-help] Cram conversion error: [main_samview] failed to write the SAM header Veronica Suaste Morales
• [Samtools-help] Extended BAQ Federico Abascal
• [Samtools-help] SAMTOOLS OPEN SOURCE? Apoorva Kulkarni
  • Re: [Samtools-help] SAMTOOLS OPEN SOURCE? James Lick
  • Re: [Samtools-help] SAMTOOLS OPEN SOURCE? Peter Cock
• [Samtools-help] samtools sort -n Rebecca Harris
  • Re: [Samtools-help] samtools sort -n Juan Daniel Montenegro Cabrera
  • Re: [Samtools-help] samtools sort -n Andrew Bjonnes
  • Re: [Samtools-help] samtools sort -n Colin Hercus
• [Samtools-help] samtools sort problem Juan Daniel Montenegro Cabrera
  • Re: [Samtools-help] samtools sort problem Juan Daniel Montenegro Cabrera
  • Re: [Samtools-help] samtools sort problem John Marshall
  • Re: [Samtools-help] samtools sort problem Juan Daniel Montenegro Cabrera
  • Re: [Samtools-help] samtools sort problem Juan Daniel Montenegro Cabrera
  • Re: [Samtools-help] samtools sort problem John Marshall
  • Re: [Samtools-help] samtools sort problem Peter Cock
  • Re: [Samtools-help] samtools sort problem Juan Daniel Montenegro Cabrera
• [Samtools-help] truncated file after reheader Seb
• [Samtools-help] bcftools view, filter on AF Tommy Carstensen
  • Re: [Samtools-help] bcftools view, filter on AF Petr Danecek
  • Re: [Samtools-help] bcftools view, filter on AF Petr Danecek
  • Re: [Samtools-help] bcftools view, filter on AF Tommy Carstensen
• [Samtools-help] Samtools data source questions Jiaming Liu
• [Samtools-help] picard-2.6.0 peijia
• [Samtools-help] Instruction to access bam files on aws s3 storage Xing Xu
  • Re: [Samtools-help] Instruction to access bam files on aws s3 storage John Marshall
• [Samtools-help] small contigs connected to be superreference 郭梁
• [Samtools-help] mpileup result in indel containing SNP Hung Chih-Ming
  • Re: [Samtools-help] mpileup result in indel containing SNP Colin Hercus
• [Samtools-help] Calling SNPs with SAMtools and BCFtools peijia
• [Samtools-help] HTSlib 1.3.2 released John Marshall
• [Samtools-help] bcftools index Segmentation fault Yuelin Zhu
  • Re: [Samtools-help] bcftools index Segmentation fault Thomas W. Blackwell
  • Re: [Samtools-help] bcftools index Segmentation fault Yuelin Zhu
  • Re: [Samtools-help] bcftools index Segmentation fault John Marshall
  • Re: [Samtools-help] bcftools index Segmentation fault John Marshall
  • Re: [Samtools-help] bcftools index Segmentation fault Yuelin Zhu
• [Samtools-help] Running samtools mpileup on BAM that contains colorspace Michael Gruenstaeudl
  • [Samtools-help] FollowUp - Running samtools mpileup on BAM that contains colorspace Michael Gruenstaeudl
  • Re: [Samtools-help] FollowUp - Running samtools mpileup on BAM that contains colorspace Colin Davenport
• [Samtools-help] Open file .tbi Gui GuiGui
  • Re: [Samtools-help] Open file .tbi Thomas W. Blackwell
  • Re: [Samtools-help] Open file .tbi Devon Ryan
• [Samtools-help] Installation problem for a new user David Siegel
  • Re: [Samtools-help] Installation problem for a new user Devon Ryan
  • Re: [Samtools-help] Installation problem for a new user Thomas W. Blackwell
  • Re: [Samtools-help] Installation problem for a new user David Siegel
• [Samtools-help] MATE_NOT_FOUND after library filtering Hannes Svardal
• [Samtools-help] samtools phase -A option not working? Kathleen Keough
• [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag James Bonfield
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag James Bonfield
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag James Bonfield
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Keiran Raine
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Keiran Raine
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Keiran Raine
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Heng Li
  • Re: [Samtools-help] samtools calmd behavior and MD tag Martin MOKREJŠ
  • Re: [Samtools-help] samtools calmd behavior and MD tag Keiran Raine
• [Samtools-help] documentation regarding samtools phase Kathleen Keough
• [Samtools-help] different output when upgrading samtools from 0.1.19 to 1.3.1 Adam Witney
  • Re: [Samtools-help] different output when upgrading samtools from 0.1.19 to 1.3.1 John Marshall
  • Re: [Samtools-help] different output when upgrading samtools from 0.1.19 to 1.3.1 Adam Witney
• [Samtools-help] bcftools merge King Wai Lau
• [Samtools-help] mpileup on a few SNPs? Tommy Carstensen
• [Samtools-help] incorrect reference bases Annie Cowell
  • Re: [Samtools-help] incorrect reference bases Thomas W. Blackwell
  • Re: [Samtools-help] incorrect reference bases John Marshall
  • Re: [Samtools-help] incorrect reference bases Colin Hercus
• [Samtools-help] Speed up VCF query by partial tbi loading CHEN Yi-Shiou
• [Samtools-help] are pair-end reads considered as orphan reads by samtools tview? 杨俊辉
• [Samtools-help] samtools confused genotype 郑竹清
• [Samtools-help] samtools with -L option hangs forever Wang, Shuoguo
• [Samtools-help] mpileup Error Julia Reisler
• [Samtools-help] bcftools annotate segfaults with tab-delimited file Roderick Yao
• [Samtools-help] pileup -vcf insertion/deletion columns Somya Khare
• [Samtools-help] Discrepancies in reported pileup read segments Lars Barquist
• [Samtools-help] I have a problem Elsayed
• [Samtools-help] BC tag question Richard Corbett
  • Re: [Samtools-help] BC tag question Nils Homer
  • Re: [Samtools-help] BC tag question Yossi Farjoun
• [Samtools-help] samtools faidx and tabix options for the regions Yongchao Ge
• [Samtools-help] Error when converting cram to bam Yvonne Teng
  • Re: [Samtools-help] Error when converting cram to bam James Bonfield
• [Samtools-help] samtools view -F/-f multiple times Dario Beraldi
  • Re: [Samtools-help] samtools view -F/-f multiple times James Bonfield
  • Re: [Samtools-help] samtools view -F/-f multiple times James Bonfield
  • Re: [Samtools-help] samtools view -F/-f multiple times Dario Beraldi
• [Samtools-help] bug in samtools mpileup? Federico Abascal
  • Re: [Samtools-help] bug in samtools mpileup? Colin Hercus
  • Re: [Samtools-help] bug in samtools mpileup? Federico Abascal
  • Re: [Samtools-help] bug in samtools mpileup? Colin Hercus
• [Samtools-help] EOF marker is absent Jens Christian Froslev Nielsen
  • Re: [Samtools-help] EOF marker is absent Peter Cock
• [Samtools-help] SNP calling in different version cause different results Sung-Huan Yu
• [Samtools-help] error building samtools-1.3.1 on mac OS X VIE
  • Re: [Samtools-help] error building samtools-1.3.1 on mac OS X James Bonfield
  • Re: [Samtools-help] error building samtools-1.3.1 on mac OS X VIE
  • Re: [Samtools-help] error building samtools-1.3.1 on mac OS X John Marshall
  • Re: [Samtools-help] error building samtools-1.3.1 on mac OS X VIE
• [Samtools-help] BGZF/Gzip variants James Bonfield
• [Samtools-help] faidx index caching Robert Davies
  • Re: [Samtools-help] faidx index caching David K Jackson
• [Samtools-help] samtools 1.3.1 max depth Lilit Nersisyan
• [Samtools-help] segfault: bcftools stats Peter Johansson
  • Re: [Samtools-help] segfault: bcftools stats Peter Johansson
  • Re: [Samtools-help] segfault: bcftools stats John Marshall
• [Samtools-help] merging BAMs without retaining sample information Yampolsky, Lev
• [Samtools-help] Question relating to samtools mpileup output Ellis Hughes
  • Re: [Samtools-help] Question relating to samtools mpileup output James Bonfield
• [Samtools-help] samtools view -L Bayazit Yunusbayev
  • Re: [Samtools-help] samtools view -L Devon Ryan
  • Re: [Samtools-help] samtools view -L Bayazit Yunusbayev
  • Re: [Samtools-help] samtools view -L Devon Ryan
  • Re: [Samtools-help] samtools view -L Bayazit Yunusbayev
• [Samtools-help] tabix giving error Arti Tandon
  • Re: [Samtools-help] tabix giving error John Marshall
• [Samtools-help] About BAM->CRAM->BAM Lin, Chih-Hsu

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