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• • Re: [Samtools-help] tabix giving error John Marshall
• [Samtools-help] About BAM->CRAM->BAM Lin, Chih-Hsu
  • Re: [Samtools-help] About BAM->CRAM->BAM James Bonfield
  • Re: [Samtools-help] About BAM->CRAM->BAM Lin, Chih-Hsu
  • Re: [Samtools-help] About BAM->CRAM->BAM jkb
• [Samtools-help] samtools view with -U option Peter Chovanec
  • Re: [Samtools-help] samtools view with -U option Keiran Raine
  • Re: [Samtools-help] samtools view with -U option Peter Chovanec
  • Re: [Samtools-help] samtools view with -U option John Marshall
  • Re: [Samtools-help] samtools view with -U option Peter Chovanec
• [Samtools-help] Empty VCF file with bcftools call Antoine Paccard
  • Re: [Samtools-help] Empty VCF file with bcftools call Petr Danecek
  • Re: [Samtools-help] Empty VCF file with bcftools call Antoine Paccard
  • Re: [Samtools-help] Empty VCF file with bcftools call Petr Danecek
  • Re: [Samtools-help] Empty VCF file with bcftools call Petr Danecek
  • Re: [Samtools-help] Empty VCF file with bcftools call Antoine Paccard
  • Re: [Samtools-help] Empty VCF file with bcftools call Petr Danecek
  • Re: [Samtools-help] Empty VCF file with bcftools call Antoine Paccard
• [Samtools-help] when installing 1.31. on Centos (redhat) linux I get bam_tview_curses.c:46:5: error: unknown type name ‘WINDOW', no obvious reason Dan Hyatt
  • Re: [Samtools-help] when installing 1.31. on Centos (redhat) linux I get bam_tview_curses.c:46:5: error: unknown type name ‘WINDOW', no obvious reason John Marshall
• [Samtools-help] DV and IDV in samtools mpileup indel calling. [email protected]
• [Samtools-help] number of mapped reads with flagstat Tagliamonte,Massimiliano S
  • Re: [Samtools-help] number of mapped reads with flagstat James Bonfield
  • Re: [Samtools-help] number of mapped reads with flagstat Tagliamonte,Massimiliano S
  • Re: [Samtools-help] number of mapped reads with flagstat John Marshall
  • Re: [Samtools-help] number of mapped reads with flagstat Andrew Bjonnes
  • Re: [Samtools-help] number of mapped reads with flagstat Tagliamonte,Massimiliano S
• [Samtools-help] Force VCF call over selected positions PLUS others Alexander Predeus
• [Samtools-help] Samtools/BCFtools/HTSlib 1.3.1 released John Marshall
• [Samtools-help] Bug in samtools version 1.3 Anne Philippi
  • Re: [Samtools-help] Bug in samtools version 1.3 Thomas W. Blackwell
  • Re: [Samtools-help] Bug in samtools version 1.3 John Marshall
• [Samtools-help] unsubscribe Colin Hercus
  • [Samtools-help] unsubscribe Þórður Kristjánsson
  • Re: [Samtools-help] unsubscribe John Marshall
• [Samtools-help] A problem of using Samtools to make VCF file liuhe （Cathy Liu）
• [Samtools-help] samtools mpileup kavita garg
  • [Samtools-help] samtools mpileup peijia
  • Re: [Samtools-help] samtools mpileup James Bonfield
• [Samtools-help] bwa samse: How to make randomness predictable? Michael Nuhn
  • Re: [Samtools-help] bwa samse: How to make randomness predictable? Michael Nuhn
• [Samtools-help] bcftools som and variant calling for exome Holly Zheng Bradley
• [Samtools-help] question about how to use Htslib to convert fastq to bam file Luyi Tian
• [Samtools-help] A question about "mpileup" Daniel Chau
  • Re: [Samtools-help] A question about "mpileup" David Jones
  • Re: [Samtools-help] A question about "mpileup" Daniel Chau
  • Re: [Samtools-help] A question about "mpileup" Colin Hercus
• [Samtools-help] When would 1.3.1 be released? Shinn Kondo
  • Re: [Samtools-help] When would 1.3.1 be released? John Marshall
• [Samtools-help] tabix wrong version Kaamesh Kamalaaharan
  • Re: [Samtools-help] tabix wrong version John Marshall
• [Samtools-help] Question of DP4 calculation for indels Yitao Tang
• [Samtools-help] Gatk und samtools Gladbach
  • Re: [Samtools-help] Gatk und samtools James Bonfield
• [Samtools-help] QUAL always 0 Adam Witney
  • Re: [Samtools-help] QUAL always 0 Petr Danecek
• Re: [Samtools-help] Samtools fastq converts Bam to Fastq with wrong read order Andrew Bjonnes
  • Re: [Samtools-help] Samtools fastq converts Bam to Fastq with wrong read order Kar Tong Tan
• [Samtools-help] Trying to fetch a read in a BAM file Claudio Alberti
  • Re: [Samtools-help] Trying to fetch a read in a BAM file Peter Johansson
  • Re: [Samtools-help] Trying to fetch a read in a BAM file Claudio Alberti
• [Samtools-help] samtools not stop Michael Peng
  • Re: [Samtools-help] samtools not stop James Bonfield
• [Samtools-help] Commands and Options - VIEW Robert May
  • Re: [Samtools-help] Commands and Options - VIEW Sven Klages
• [Samtools-help] mpileup - [E..hts_open_format] error Wybouw, Nicky
  • Re: [Samtools-help] mpileup - [E..hts_open_format] error John Marshall
• [Samtools-help] Recommended guidelines for SNP detection in single-cells Trevor Tanner
• [Samtools-help] Command DEPTH Options Robert May
  • Re: [Samtools-help] Command DEPTH Options Peter Cock
• [Samtools-help] Trying to fetch the mate in a BAM file Claudio Alberti
• [Samtools-help] samtools sort output carol white
  • Re: [Samtools-help] samtools sort output Tommy Carstensen
• [Samtools-help] samtools PL [email protected]
  • Re: [Samtools-help] samtools PL Tommy Carstensen
• [Samtools-help] -N setting Ryan Kevin (GUY'S AND ST THOMAS' NHS FOUNDATION TRUST)
  • Re: [Samtools-help] -N setting John Marshall
• [Samtools-help] questions about options -m -f -B of command samtools view Jing meng
  • Re: [Samtools-help] questions about options -m -f -B of command samtools view Andrew Bjonnes
  • Re: [Samtools-help] questions about options -m -f -B of command samtools view James Bonfield
  • Re: [Samtools-help] questions about options -m -f -B of command samtools view Jing meng
• [Samtools-help] Samtools IDXSTATS Margaret Linan MPH
  • Re: [Samtools-help] Samtools IDXSTATS Peter Cock
• [Samtools-help] picard tools error Giulia
  • Re: [Samtools-help] picard tools error Dario Beraldi
  • Re: [Samtools-help] picard tools error Giulia
  • Re: [Samtools-help] picard tools error Andrew Bjonnes
  • Re: [Samtools-help] picard tools error Dario Beraldi
  • Re: [Samtools-help] picard tools error Giulia
• [Samtools-help] gzopen64 error William Hsiao
  • Re: [Samtools-help] gzopen64 error John Marshall
  • Re: [Samtools-help] gzopen64 error William Hsiao
  • Re: [Samtools-help] gzopen64 error John Marshall
  • Re: [Samtools-help] gzopen64 error William Hsiao
  • Re: [Samtools-help] gzopen64 error John Marshall
• [Samtools-help] Mpileup with neighbouring indels James Bonfield
  • Re: [Samtools-help] Mpileup with neighbouring indels Hideo Imamura
• [Samtools-help] rmdup Segmentation Fault Friedman, Ryan
  • Re: [Samtools-help] rmdup Segmentation Fault Devon Ryan
  • Re: [Samtools-help] rmdup Segmentation Fault John Marshall
  • Re: [Samtools-help] rmdup Segmentation Fault James Bonfield
• [Samtools-help] error building samtools 1.3 Stephane Plaisance
  • Re: [Samtools-help] error building samtools 1.3 John Marshall
  • [Samtools-help] error building htslib 1.3 on mac OS X (macports) Stephane Plaisance
  • Re: [Samtools-help] error building htslib 1.3 on mac OS X (macports) John Marshall
• [Samtools-help] Mpileup format James Bonfield
• [Samtools-help] Picard MarkDuplicates error: Value was put into PairInfoMap more than once Nitin Bhardwaj
  • Re: [Samtools-help] Picard MarkDuplicates error: Value was put into PairInfoMap more than once Richard Corbett
  • Re: [Samtools-help] Picard MarkDuplicates error: Value was put into PairInfoMap more than once Keiran Raine
• [Samtools-help] Ns in vcfutils.pl Joanna Kelley
• [Samtools-help] samtools mpileup genotype likelihood calulation Günter Jäger
  • Re: [Samtools-help] samtools mpileup genotype likelihood calulation Thomas W. Blackwell
  • Re: [Samtools-help] samtools mpileup genotype likelihood calulation Petr Danecek
  • Re: [Samtools-help] samtools mpileup genotype likelihood calulation Petr Danecek
• [Samtools-help] fastq/a samtools command error fault Robert May
  • Re: [Samtools-help] fastq/a samtools command error fault Sendu Bala
• [Samtools-help] HTSlib API to count BAM records related to one reference Claudio Alberti
  • Re: [Samtools-help] HTSlib API to count BAM records related to one reference Thomas W. Blackwell
  • Re: [Samtools-help] HTSlib API to count BAM records related to one reference Claudio Alberti
  • Re: [Samtools-help] HTSlib API to count BAM records related to one reference John Marshall
  • Re: [Samtools-help] HTSlib API to count BAM records related to one reference Claudio Alberti
• [Samtools-help] Query on Samtools view downsample shruti kane
• [Samtools-help] Updated Cygwin64 with 2.4.1.1 Robert May
• [Samtools-help] Samtools make no rule to make target kfunc stop Robert May
• [Samtools-help] BCFTools make errors Robert May
• [Samtools-help] SAMTOOLS make install error Robert May
• [Samtools-help] samtools rmdup for variant calling with GATK Svyatoslav Sidorov
• [Samtools-help] samtools fastq carol white
  • Re: [Samtools-help] samtools fastq Bob Harris
  • Re: [Samtools-help] samtools fastq Peter Cock
• Re: [Samtools-help] Samtools makefile error James Bonfield
  • Re: [Samtools-help] Samtools makefile error Robert May
  • Re: [Samtools-help] Samtools makefile error James Bonfield
  • Re: [Samtools-help] Samtools makefile error James Bonfield
• [Samtools-help] Meaning of TC aux tag James Bonfield
• [Samtools-help] Indexed read retrieval with -L Stephane Castel
• [Samtools-help] bcftools Error Guertin, Michael J. (mjg7y)
  • Re: [Samtools-help] bcftools Error Petr Danecek
  • [Samtools-help] bcftools Error Kousik Kundu
• [Samtools-help] statistical method of samtools and bcftools ??????
• Re: [Samtools-help] bam2depth compile separately Heng Li
  • [Samtools-help] 答复: bam2depth compile separately Zengquan He
  • [Samtools-help] Windows10 cygwin64 and samtools problem installing Robert May
  • Re: [Samtools-help] Windows10 cygwin64 and samtools problem installing John Marshall
  • Re: [Samtools-help] Windows10 cygwin64 and samtools problem installing Robert May
• [Samtools-help] building error under OS X 10.10.5 with macport Stephane Plaisance | VIB |
  • Re: [Samtools-help] building error under OS X 10.10.5 with macport John Marshall
• [Samtools-help] Samtools/BCFtools/HTSlib 1.3 released John Marshall
  • Re: [Samtools-help] Samtools/BCFtools/HTSlib 1.3 released Liu Xingliang
• [Samtools-help] samtools stats: definition of insert size average Dieter Best
• [Samtools-help] best way to approximate the old school pileup Richard Corbett
  • Re: [Samtools-help] best way to approximate the old school pileup James Bonfield
  • Re: [Samtools-help] best way to approximate the old school pileup Richard Corbett
• [Samtools-help] BWA HLA Fatima Naveed
• [Samtools-help] samtools index fails to open the BAM file Yampolsky, Lev
  • Re: [Samtools-help] samtools index fails to open the BAM file Douglas Senalik
• [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file James Bonfield
  • Re: [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file James Bonfield
  • Re: [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file James Bonfield
  • Re: [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file John Marshall
  • Re: [Samtools-help] Seek and tell a BAM file Chad S Harland
  • Re: [Samtools-help] Seek and tell a BAM file Claudio Alberti
  • Re: [Samtools-help] Seek and tell a BAM file John Marshall
• [Samtools-help] bcftools annotate Tagliamonte,Massimiliano S
• [Samtools-help] I cam cross a problem in compiling the C script using the samtools api hgong
  • Re: [Samtools-help] I cam cross a problem in compiling the C script using the samtools api John Marshall
• [Samtools-help] functionality to edit flag? Ni Huang
• [Samtools-help] bcftools annotate segfaults with bed file Alessandro Mammana
  • Re: [Samtools-help] bcftools annotate segfaults with bed file Petr Danecek
• [Samtools-help] Piping samtools output to picard Yaseen Ladak
  • Re: [Samtools-help] Piping samtools output to picard Devon Ryan
  • Re: [Samtools-help] Piping samtools output to picard Yaseen Ladak
  • Re: [Samtools-help] Piping samtools output to picard Devon Ryan
  • Re: [Samtools-help] Piping samtools output to picard Yaseen Ladak
• [Samtools-help] Missing stdarg.h in cram.h when compiling samtools Ivo Palli
  • Re: [Samtools-help] Missing stdarg.h in cram.h when compiling samtools John Marshall
• [Samtools-help] Uniquely mapping reads in mpileup Wright, Alison
  • Re: [Samtools-help] Uniquely mapping reads in mpileup Petr Danecek
  • Re: [Samtools-help] Uniquely mapping reads in mpileup Wright, Alison
  • Re: [Samtools-help] Uniquely mapping reads in mpileup Petr Danecek
  • Re: [Samtools-help] Uniquely mapping reads in mpileup James Bonfield
  • Re: [Samtools-help] Uniquely mapping reads in mpileup Wright, Alison
• [Samtools-help] I can't make Samtools from the Makefile Xavier Olessa-Dragon
  • Re: [Samtools-help] I can't make Samtools from the Makefile Thomas W. Blackwell
  • Re: [Samtools-help] I can't make Samtools from the Makefile Christian Cole (Staff)
• [Samtools-help] samtools sort segmentation fault Marie Kroeger
• [Samtools-help] bgzip from Java code? Terry Casstevens
  • Re: [Samtools-help] [Samtools-devel] bgzip from Java code? Nils Homer
• [Samtools-help] Reading Custom Index - Creates many threads? Terry Casstevens
• [Samtools-help] Cygwin installation of SamTools Christopher Wozniak
• [Samtools-help] Installation problems on Windows Christopher Wozniak
  • Re: [Samtools-help] Installation problems on Windows Karel Břinda
• [Samtools-help] pileup format ?? Norge Cruz Hernández
• [Samtools-help] bgzip performance? Terry Casstevens
  • Re: [Samtools-help] [Samtools-devel] bgzip performance? Nils Homer

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