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• • Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Salzberg, Anna
  • Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Heng Li
  • Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Heng Li
  • Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Nils Homer
• [Samtools-help] read qual distr William Gilks
  • Re: [Samtools-help] read qual distr Tim Fennell
  • Re: [Samtools-help] read qual distr Heng Li
• [Samtools-help] bcftools filtering mehar
  • [Samtools-help] bcftools filtering Ciaran O'Flynn
  • Re: [Samtools-help] bcftools filtering Arumilli, Meharji
• [Samtools-help] Picard Release 1.122 George Grant
  • Re: [Samtools-help] Picard Release 1.122 Rusch, Michael
  • Re: [Samtools-help] Picard Release 1.122 Louis Letourneau
  • Re: [Samtools-help] Picard Release 1.122 Nils Homer
  • Re: [Samtools-help] Picard Release 1.122 Louis Letourneau
• [Samtools-help] HardFiltering variants mehar
  • Re: [Samtools-help] HardFiltering variants Tim Fennell
  • Re: [Samtools-help] HardFiltering variants mehar
  • Re: [Samtools-help] HardFiltering variants mehar
  • Re: [Samtools-help] HardFiltering variants Petr Danecek
• [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics Konstantinos Mavrommatis
  • Re: [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics John Damm Sørensen
  • Re: [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics Nils Homer
• [Samtools-help] samtools V1.1 DPR option Koh, Chushin
  • Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
  • Re: [Samtools-help] samtools V1.1 DPR option Koh, Chushin
  • Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
  • Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
• [Samtools-help] How to create consensus sequence Sami Pietilä
  • Re: [Samtools-help] How to create consensus sequence Colin Hercus
  • Re: [Samtools-help] How to create consensus sequence Sami Pietilä
  • Re: [Samtools-help] How to create consensus sequence Colin Hercus
  • Re: [Samtools-help] How to create consensus sequence Sami Pietilä
  • Re: [Samtools-help] How to create consensus sequence Sami Pietilä
  • Re: [Samtools-help] How to create consensus sequence Colin Hercus
  • Re: [Samtools-help] How to create consensus sequence Sami Pietilä
• [Samtools-help] Core dump when calling samtools index Derek M.
  • Re: [Samtools-help] Core dump when calling samtools index John Marshall
  • Re: [Samtools-help] Core dump when calling samtools index Derek M.
• [Samtools-help] Issue with selecting specific regions with Tabix Machiela, Mitchell (NIH/NCI) [F]
  • Re: [Samtools-help] Issue with selecting specific regions with Tabix Thomas W. Blackwell
• [Samtools-help] CalculateHsMetrics Ryan G
  • Re: [Samtools-help] CalculateHsMetrics Nils Homer
• [Samtools-help] documentation for releases from 0.1.20 to 1.1 Sukhadia, Shrey S
• [Samtools-help] OPT variables that that changed in CRAM format ? Kees-Jan Francoijs
• [Samtools-help] large fragmented reference genome Koh, Chushin
  • Re: [Samtools-help] large fragmented reference genome Thomas Keane
• [Samtools-help] picard_MarkDuplicates:Exception closing FileOutputStream Mengmeng Lu
  • Re: [Samtools-help] picard_MarkDuplicates:Exception closing FileOutputStream Thomas Sibley
• [Samtools-help] samtools variant calling on pedigree samples Amy Williams
• [Samtools-help] Tools to remove read given region? Wibowo Arindrarto
  • Re: [Samtools-help] Tools to remove read given region? Nils Homer
  • Re: [Samtools-help] Tools to remove read given region? Mike Lindberg
  • Re: [Samtools-help] Tools to remove read given region? Mike Lindberg
  • Re: [Samtools-help] Tools to remove read given region? Wibowo Arindrarto
• [Samtools-help] Hard to do language bindings in samtools-1.1 Lincoln Stein
• [Samtools-help] samtools idxstats produces incorrect values for cram Saunders, Chris
• [Samtools-help] Samtools view -X Nils Homer
  • Re: [Samtools-help] Samtools view -X John Marshall
  • Re: [Samtools-help] Samtools view -X Nils Homer
• [Samtools-help] samtools/bcftools/htslib 1.1 released John Marshall
  • Re: [Samtools-help] samtools/bcftools/htslib 1.1 released Lo, Chien-Chi
• Re: [Samtools-help] LD removed from BCFTools? Adrian Pelin
  • Re: [Samtools-help] LD removed from BCFTools? Petr Danecek
• [Samtools-help] samtools and picard - removing duplicates John Duce
  • Re: [Samtools-help] samtools and picard - removing duplicates Tim Fennell
• [Samtools-help] Picard release 1.121 Bradley Taylor
• [Samtools-help] [bam_sort_core] truncated file. Continue anyway Vickie S
  • Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Bob Harris
  • Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Vickie S
  • Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Colin Hercus
  • Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Nils Homer
• [Samtools-help] Samtools call SNP Sung-Huan Yu
  • Re: [Samtools-help] Samtools call SNP Devon Ryan
  • Re: [Samtools-help] Samtools call SNP Sung-Huan Yu
  • Re: [Samtools-help] Samtools call SNP Devon Ryan
  • Re: [Samtools-help] Samtools call SNP Sung-Huan Yu
• [Samtools-help] SAM/BAM format versions Wolfgang Maier
• [Samtools-help] Make error Paul Darbyshire
  • [Samtools-help] Make error Guillermo Parada
  • Re: [Samtools-help] Make error Devon Ryan
  • Re: [Samtools-help] Make error Devon Ryan
• [Samtools-help] Samtools View Can Make Command Line Unresponsive Dario Strbenac
  • Re: [Samtools-help] Samtools View Can Make Command Line Unresponsive Peter Johansson
• [Samtools-help] Losing reads with Picard Sam2Fastq Justin P Whalley
  • Re: [Samtools-help] Losing reads with Picard Sam2Fastq Tim Fennell
  • Re: [Samtools-help] Losing reads with Picard Sam2Fastq Justin P Whalley
• [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Kanterakis, Efstathios
  • Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Nils Homer
  • Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Kanterakis, Efstathios
  • Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Nils Homer
• [Samtools-help] CollectHsMetrics Low/Zero MQ reads Gowrisankar, Sivakumar
  • Re: [Samtools-help] CollectHsMetrics Low/Zero MQ reads Nils Homer
• [Samtools-help] ##contig header lines in samtools-1.0 SNP calling output Wolfgang Maier
  • Re: [Samtools-help] ##contig header lines in samtools-1.0 SNP calling output Petr Danecek
• [Samtools-help] What commands of samtools are related with Li 2011 paper? Peng Yu
• [Samtools-help] Picard ValidateSamFile error Eric Roller
  • [Samtools-help] Picard ValidateSamFile error Eric Roller
  • Re: [Samtools-help] Picard ValidateSamFile error Tim Fennell
  • Re: [Samtools-help] Picard ValidateSamFile error Nils Homer
  • Re: [Samtools-help] Picard ValidateSamFile error Eric Roller
• [Samtools-help] Samtools Compression Level Dario Strbenac
  • Re: [Samtools-help] Samtools Compression Level John Marshall
• [Samtools-help] sort Command Requires Unnecessary Option Dario Strbenac
• [Samtools-help] Count in soft clipped reads for discordant call Aparna
  • Re: [Samtools-help] Count in soft clipped reads for discordant call Petr Danecek
  • Re: [Samtools-help] Count in soft clipped reads for discordant call Petr Danecek
• [Samtools-help] Please stop sending me mails Mónica Fabbro
  • Re: [Samtools-help] Please stop sending me mails Mark T. W. Ebbert
• [Samtools-help] picard tool emits stack guard warning Lionel Brooks
  • Re: [Samtools-help] picard tool emits stack guard warning Nils Homer
• [Samtools-help] Intrasamle diversity and allele support Tagliamonte,Massimiliano S
  • Re: [Samtools-help] Intrasamle diversity and allele support Thomas W. Blackwell
  • Re: [Samtools-help] Intrasamle diversity and allele support Tagliamonte,Massimiliano S
  • Re: [Samtools-help] Intrasamle diversity and allele support Petr Danecek
• [Samtools-help] samtools DP and DP4 Arumilli, Meharji
  • Re: [Samtools-help] samtools DP and DP4 Xiaobin Xing
• [Samtools-help] tweak_overlap_quality Brent Pedersen
  • Re: [Samtools-help] tweak_overlap_quality Petr Danecek
• [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jan Taylor
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Thomas W. Blackwell
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Nils Homer
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jan Taylor
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Bob Handsaker
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jeff Gentry
  • Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Christian Cole
• [Samtools-help] Issue with ValidateSamFile María Teresa Chávez
  • Re: [Samtools-help] Issue with ValidateSamFile Nils Homer
• [Samtools-help] Problem running Picard MarkDuplicates Asa Perez-Bercoff
  • Re: [Samtools-help] Problem running Picard MarkDuplicates Kathleen Tibbetts
• [Samtools-help] mate inner distance Laurent MANCHON
  • Re: [Samtools-help] mate inner distance Thomas W. Blackwell
  • Re: [Samtools-help] mate inner distance Monica Britton
• [Samtools-help] picard markduplicates and supplementary alignments Ni Huang
  • Re: [Samtools-help] picard markduplicates and supplementary alignments Nils Homer
  • Re: [Samtools-help] picard markduplicates and supplementary alignments Nils Homer
  • Re: [Samtools-help] picard markduplicates and supplementary alignments Ni Huang
  • Re: [Samtools-help] picard markduplicates and supplementary alignments John Marshall
• [Samtools-help] A wish for restored functionality Rasmus Borup Hansen
• [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Trakhtenberg, Feliks
  • Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
  • Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
  • Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Trakhtenberg, Feliks
  • Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
  • Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Jeremy Volkening
• [Samtools-help] Samtools sort (merging) is slow Adam Skarshewski
  • Re: [Samtools-help] Samtools sort (merging) is slow John Marshall
  • Re: [Samtools-help] Samtools sort (merging) is slow Adam Skarshewski
• [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B BJ Chen
  • Re: [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B Petr Danecek
  • Re: [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B BJ Chen
• [Samtools-help] SamToFastq: found unpaired mates Joshua Gould
  • Re: [Samtools-help] SamToFastq: found unpaired mates Ogan
• [Samtools-help] samples' order in mpileup Yampolsky, Lev
  • Re: [Samtools-help] samples' order in mpileup Devon Ryan
• [Samtools-help] What are the difference between 'view' options (-F , -f)? Dror Hibsh
  • Re: [Samtools-help] What are the difference between 'view' options (-F , -f)? Petr Danecek
• [Samtools-help] Samtools sort -n problems Mark Wadsworth
  • Re: [Samtools-help] Samtools sort -n problems Devon Ryan
• [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
  • Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Nils Homer
  • Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
  • Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Nils Homer
  • Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
• [Samtools-help] cram usage Radhouane Aniba
  • Re: [Samtools-help] cram usage Radhouane Aniba
  • Re: [Samtools-help] cram usage Praveen Raj
• [Samtools-help] samtools 1.0 install problem Radhouane Aniba
  • Re: [Samtools-help] samtools 1.0 install problem Praveen Raj
  • Re: [Samtools-help] samtools 1.0 install problem Radhouane Aniba
  • Re: [Samtools-help] samtools 1.0 install problem Sam Nicholls
• Re: [Samtools-help] bgzf buffering Louis Letourneau
• [Samtools-help] An problem on replace header of bam file by using samtools jiey...@annoroad.com
  • Re: [Samtools-help] An problem on replace header of bam file by using samtools Colin Hercus
• [Samtools-help] samtools/bcftools strange (error ?) lack of call Mathieu Bourgey
  • Re: [Samtools-help] samtools/bcftools strange (error ?) lack of call Petr Danecek
• [Samtools-help] Picard release 1.119 Bradley Taylor
  • Re: [Samtools-help] Picard release 1.119 Bradley Taylor
• [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
  • Re: [Samtools-help] Trouble indexing a very large VCF file Laura Clarke
  • Re: [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
  • Re: [Samtools-help] Trouble indexing a very large VCF file Tim Fennell
  • Re: [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
• [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? James Nemesh
  • Re: [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? Jim Robinson
  • Re: [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? James Nemesh
• [Samtools-help] Picard-Removing Duplicates Ankur Naqib
• [Samtools-help] SAMFormatException: "...bin field of BAM record does not equal value computed based on alignment start and end..." Mark Ebbert
  • Re: [Samtools-help] SAMFormatException: "...bin field of BAM record does not equal value computed based on alignment start and end..." Mark T. W. Ebbert
• [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Nils Homer
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Bob Handsaker
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Mark Ebbert
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley

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