samtools-help

Messages by Date

2014/10/14 Re: [Samtools-help] samtools reheader causes terminal to flicker Peter Cock
2014/10/14 [Samtools-help] samtools reheader causes terminal to flicker Joshua Theisen
2014/10/14 [Samtools-help] strand bias threshold value Arumilli, Meharji
2014/10/14 Re: [Samtools-help] [bcf_sync] incorrect number of fields Petr Danecek
2014/10/13 [Samtools-help] MarkDuplicates output Ryan G
2014/10/12 [Samtools-help] Meaning of BAQ 0 in given context Andreas Wilm
2014/10/10 Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Nils Homer
2014/10/10 Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Salzberg, Anna
2014/10/10 Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Salzberg, Anna
2014/10/10 [Samtools-help] Samtools vs GATK functionality Lau, Branden M - (bmlau)
2014/10/09 [Samtools-help] [bcf_sync] incorrect number of fields Casper Shyr
2014/10/09 Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Nils Homer
2014/10/09 Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Nils Homer
2014/10/09 Re: [Samtools-help] bcftools filtering Arumilli, Meharji
2014/10/09 [Samtools-help] Tracking changes in versions Sukhadia, Shrey S
2014/10/09 [Samtools-help] bcftools filtering Ciaran O'Flynn
2014/10/09 [Samtools-help] Reporting Bug - Optical Duplicates of Picard MarkDuplicates Salzberg, Anna
2014/10/09 Re: [Samtools-help] How to create consensus sequence Sami Pietilä
2014/10/09 Re: [Samtools-help] Picard Release 1.122 Louis Letourneau
2014/10/09 Re: [Samtools-help] Picard Release 1.122 Nils Homer
2014/10/09 Re: [Samtools-help] Picard Release 1.122 Louis Letourneau
2014/10/09 Re: [Samtools-help] read qual distr Heng Li
2014/10/09 Re: [Samtools-help] read qual distr Tim Fennell
2014/10/09 [Samtools-help] read qual distr William Gilks
2014/10/09 Re: [Samtools-help] Picard Release 1.122 Rusch, Michael
2014/10/09 Re: [Samtools-help] How to create consensus sequence Colin Hercus
2014/10/09 [Samtools-help] bcftools filtering mehar
2014/10/09 Re: [Samtools-help] How to create consensus sequence Sami Pietilä
2014/10/09 Re: [Samtools-help] HardFiltering variants Petr Danecek
2014/10/09 Re: [Samtools-help] HardFiltering variants mehar
2014/10/09 Re: [Samtools-help] HardFiltering variants mehar
2014/10/08 Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
2014/10/08 [Samtools-help] Picard Release 1.122 George Grant
2014/10/08 Re: [Samtools-help] HardFiltering variants Tim Fennell
2014/10/08 Re: [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics Nils Homer
2014/10/08 [Samtools-help] HardFiltering variants mehar
2014/10/08 Re: [Samtools-help] How to create consensus sequence Sami Pietilä
2014/10/08 Re: [Samtools-help] How to create consensus sequence Colin Hercus
2014/10/08 Re: [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics John Damm Sørensen
2014/10/08 [Samtools-help] Problems with picard 1.119. CollectAlignmentMetrics and CollectInsertSizeMetrics Konstantinos Mavrommatis
2014/10/08 Re: [Samtools-help] How to create consensus sequence Sami Pietilä
2014/10/07 Re: [Samtools-help] How to create consensus sequence Colin Hercus
2014/10/07 Re: [Samtools-help] CalculateHsMetrics Nils Homer
2014/10/07 Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
2014/10/07 Re: [Samtools-help] samtools V1.1 DPR option Petr Danecek
2014/10/07 Re: [Samtools-help] samtools V1.1 DPR option Koh, Chushin
2014/10/07 [Samtools-help] samtools V1.1 DPR option Koh, Chushin
2014/10/07 Re: [Samtools-help] Core dump when calling samtools index Derek M.
2014/10/07 [Samtools-help] How to create consensus sequence Sami Pietilä
2014/10/07 Re: [Samtools-help] Issue with selecting specific regions with Tabix Thomas W. Blackwell
2014/10/07 Re: [Samtools-help] Core dump when calling samtools index John Marshall
2014/10/07 [Samtools-help] Core dump when calling samtools index Derek M.
2014/10/07 [Samtools-help] Issue with selecting specific regions with Tabix Machiela, Mitchell (NIH/NCI) [F]
2014/10/06 [Samtools-help] CalculateHsMetrics Ryan G
2014/10/03 Re: [Samtools-help] mpileup output confusion jbr950
2014/10/03 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/10/02 Re: [Samtools-help] mpileup output confusion jbr950
2014/10/02 [Samtools-help] documentation for releases from 0.1.20 to 1.1 Sukhadia, Shrey S
2014/10/02 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/10/01 Re: [Samtools-help] mpileup output confusion jbr950
2014/10/01 [Samtools-help] OPT variables that that changed in CRAM format ? Kees-Jan Francoijs
2014/10/01 Re: [Samtools-help] Tools to remove read given region? Wibowo Arindrarto
2014/09/30 Re: [Samtools-help] Tools to remove read given region? Mike Lindberg
2014/09/30 Re: [Samtools-help] Tools to remove read given region? Mike Lindberg
2014/09/30 Re: [Samtools-help] Tools to remove read given region? Nils Homer
2014/09/30 Re: [Samtools-help] samtools/bcftools/htslib 1.1 released Lo, Chien-Chi
2014/09/30 Re: [Samtools-help] picard_MarkDuplicates:Exception closing FileOutputStream Thomas Sibley
2014/09/30 Re: [Samtools-help] large fragmented reference genome Thomas Keane
2014/09/30 [Samtools-help] large fragmented reference genome Koh, Chushin
2014/09/29 [Samtools-help] picard_MarkDuplicates:Exception closing FileOutputStream Mengmeng Lu
2014/09/29 [Samtools-help] samtools variant calling on pedigree samples Amy Williams
2014/09/29 [Samtools-help] Tools to remove read given region? Wibowo Arindrarto
2014/09/26 [Samtools-help] Hard to do language bindings in samtools-1.1 Lincoln Stein
2014/09/26 [Samtools-help] samtools idxstats produces incorrect values for cram Saunders, Chris
2014/09/25 Re: [Samtools-help] Samtools view -X Nils Homer
2014/09/25 Re: [Samtools-help] Samtools view -X John Marshall
2014/09/25 [Samtools-help] Samtools view -X Nils Homer
2014/09/25 Re: [Samtools-help] LD removed from BCFTools? Petr Danecek
2014/09/24 Re: [Samtools-help] samtools and picard - removing duplicates Tim Fennell
2014/09/23 [Samtools-help] samtools/bcftools/htslib 1.1 released John Marshall
2014/09/23 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/09/23 Re: [Samtools-help] mpileup output confusion jbr950
2014/09/23 Re: [Samtools-help] LD removed from BCFTools? Adrian Pelin
2014/09/23 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/09/23 Re: [Samtools-help] mpileup output confusion jbr950
2014/09/23 [Samtools-help] samtools and picard - removing duplicates John Duce
2014/09/22 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/09/22 Re: [Samtools-help] CollectHsMetrics Low/Zero MQ reads Nils Homer
2014/09/22 Re: [Samtools-help] picard tool emits stack guard warning Nils Homer
2014/09/22 [Samtools-help] Picard release 1.121 Bradley Taylor
2014/09/22 Re: [Samtools-help] mpileup output confusion jbr950
2014/09/22 Re: [Samtools-help] Samtools call SNP Sung-Huan Yu
2014/09/22 Re: [Samtools-help] Samtools call SNP Devon Ryan
2014/09/22 Re: [Samtools-help] Samtools call SNP Sung-Huan Yu
2014/09/21 Re: [Samtools-help] Samtools call SNP Devon Ryan
2014/09/20 Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Nils Homer
2014/09/19 Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Colin Hercus
2014/09/19 Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Bob Harris
2014/09/19 Re: [Samtools-help] [bam_sort_core] truncated file. Continue anyway Vickie S
2014/09/19 [Samtools-help] [bam_sort_core] truncated file. Continue anyway Vickie S
2014/09/19 [Samtools-help] Samtools call SNP Sung-Huan Yu
2014/09/19 [Samtools-help] SAM/BAM format versions Wolfgang Maier
2014/09/18 [Samtools-help] Make error Paul Darbyshire
2014/09/18 Re: [Samtools-help] Losing reads with Picard Sam2Fastq Justin P Whalley
2014/09/18 Re: [Samtools-help] picard markduplicates and supplementary alignments John Marshall
2014/09/18 Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Nils Homer
2014/09/18 Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Kanterakis, Efstathios
2014/09/17 Re: [Samtools-help] Samtools View Can Make Command Line Unresponsive Peter Johansson
2014/09/17 [Samtools-help] Samtools View Can Make Command Line Unresponsive Dario Strbenac
2014/09/17 Re: [Samtools-help] picard markduplicates and supplementary alignments Ni Huang
2014/09/17 Re: [Samtools-help] picard markduplicates and supplementary alignments Nils Homer
2014/09/17 Re: [Samtools-help] Issue with ValidateSamFile Nils Homer
2014/09/17 Re: [Samtools-help] Losing reads with Picard Sam2Fastq Tim Fennell
2014/09/17 [Samtools-help] Losing reads with Picard Sam2Fastq Justin P Whalley
2014/09/16 Re: [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Nils Homer
2014/09/16 [Samtools-help] CollectTargetedPcrMetrics concatenates overlapping intervals Kanterakis, Efstathios
2014/09/15 [Samtools-help] CollectHsMetrics Low/Zero MQ reads Gowrisankar, Sivakumar
2014/09/15 Re: [Samtools-help] ##contig header lines in samtools-1.0 SNP calling output Petr Danecek
2014/09/15 [Samtools-help] ##contig header lines in samtools-1.0 SNP calling output Wolfgang Maier
2014/09/15 Re: [Samtools-help] Count in soft clipped reads for discordant call Petr Danecek
2014/09/15 Re: [Samtools-help] Intrasamle diversity and allele support Petr Danecek
2014/09/15 Re: [Samtools-help] tweak_overlap_quality Petr Danecek
2014/09/15 Re: [Samtools-help] Count in soft clipped reads for discordant call Petr Danecek
2014/09/12 [Samtools-help] What commands of samtools are related with Li 2011 paper? Peng Yu
2014/09/12 Re: [Samtools-help] Picard ValidateSamFile error Eric Roller
2014/09/12 Re: [Samtools-help] Picard ValidateSamFile error Nils Homer
2014/09/12 Re: [Samtools-help] Picard ValidateSamFile error Tim Fennell
2014/09/11 [Samtools-help] Picard ValidateSamFile error Eric Roller
2014/09/11 Re: [Samtools-help] Samtools Compression Level John Marshall
2014/09/11 [Samtools-help] Picard ValidateSamFile error Eric Roller
2014/09/11 [Samtools-help] Samtools Compression Level Dario Strbenac
2014/09/11 [Samtools-help] sort Command Requires Unnecessary Option Dario Strbenac
2014/09/09 [Samtools-help] Count in soft clipped reads for discordant call Aparna
2014/09/09 Re: [Samtools-help] Please stop sending me mails Mark T. W. Ebbert
2014/09/09 [Samtools-help] Please stop sending me mails Mónica Fabbro
2014/09/09 [Samtools-help] picard tool emits stack guard warning Lionel Brooks
2014/09/09 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jeff Gentry
2014/09/09 Re: [Samtools-help] Intrasamle diversity and allele support Tagliamonte,Massimiliano S
2014/09/09 Re: [Samtools-help] Intrasamle diversity and allele support Thomas W. Blackwell
2014/09/09 [Samtools-help] Intrasamle diversity and allele support Tagliamonte,Massimiliano S
2014/09/09 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Bob Handsaker
2014/09/09 Re: [Samtools-help] samtools DP and DP4 Xiaobin Xing
2014/09/09 [Samtools-help] samtools DP and DP4 Arumilli, Meharji
2014/09/09 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jan Taylor
2014/09/08 Re: [Samtools-help] Picard release 1.119 Bradley Taylor
2014/09/08 [Samtools-help] tweak_overlap_quality Brent Pedersen
2014/09/08 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Christian Cole
2014/09/08 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Nils Homer
2014/09/08 Re: [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Thomas W. Blackwell
2014/09/08 [Samtools-help] picard CalculateHSMetrics error 'Ignoring interval for unknown reference' Jan Taylor
2014/09/08 Re: [Samtools-help] Problem running Picard MarkDuplicates Kathleen Tibbetts
2014/09/08 [Samtools-help] Issue with ValidateSamFile María Teresa Chávez
2014/09/08 [Samtools-help] Problem running Picard MarkDuplicates Asa Perez-Bercoff
2014/09/05 Re: [Samtools-help] Samtools sort (merging) is slow Adam Skarshewski
2014/09/05 Re: [Samtools-help] mate inner distance Monica Britton
2014/09/05 Re: [Samtools-help] mate inner distance Thomas W. Blackwell
2014/09/05 [Samtools-help] mate inner distance Laurent MANCHON
2014/09/05 Re: [Samtools-help] picard markduplicates and supplementary alignments Nils Homer
2014/09/05 [Samtools-help] picard markduplicates and supplementary alignments Ni Huang
2014/09/05 Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Jeremy Volkening
2014/09/05 Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
2014/09/05 Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Trakhtenberg, Feliks
2014/09/05 Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
2014/09/05 Re: [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Nils Homer
2014/09/05 [Samtools-help] A wish for restored functionality Rasmus Borup Hansen
2014/09/05 Re: [Samtools-help] Samtools sort (merging) is slow John Marshall
2014/09/05 [Samtools-help] Picard error Illegal Mate State in converting Tophat BAM output to Fastq Trakhtenberg, Feliks
2014/09/05 [Samtools-help] Samtools sort (merging) is slow Adam Skarshewski
2014/09/04 Re: [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B BJ Chen
2014/09/04 Re: [Samtools-help] segmentation fault when running mpileup with -f Petr Danecek
2014/09/04 Re: [Samtools-help] mpileup output confusion Petr Danecek
2014/09/04 Re: [Samtools-help] multiple ALT alleles Petr Danecek
2014/09/04 Re: [Samtools-help] IO file handle support for bgzipped VCF files Petr Danecek
2014/09/04 Re: [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B Petr Danecek
2014/09/04 Re: [Samtools-help] htslib C API Petr Danecek
2014/09/04 Re: [Samtools-help] What are the difference between 'view' options (-F , -f)? Petr Danecek
2014/09/04 Re: [Samtools-help] samtools/bcftools strange (error ?) lack of call Petr Danecek
2014/09/03 [Samtools-help] samtools 1.0 mpileup: strange base quality, even with -B BJ Chen
2014/09/03 [Samtools-help] SamToFastq: found unpaired mates Joshua Gould
2014/09/02 Re: [Samtools-help] SAMFormatException: "...bin field of BAM record does not equal value computed based on alignment start and end..." Mark T. W. Ebbert
2014/09/01 Re: [Samtools-help] samples' order in mpileup Devon Ryan
2014/09/01 [Samtools-help] samples' order in mpileup Yampolsky, Lev
2014/08/31 [Samtools-help] What are the difference between 'view' options (-F , -f)? Dror Hibsh
2014/08/28 Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
2014/08/28 Re: [Samtools-help] Samtools sort -n problems Devon Ryan
2014/08/28 [Samtools-help] Samtools sort -n problems Mark Wadsworth
2014/08/28 Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Nils Homer
2014/08/28 Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
2014/08/28 Re: [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Nils Homer
2014/08/28 [Samtools-help] CollectAlignmentSummaryMetrics reports zero aligned reads Jeremy Volkening
2014/08/28 Re: [Samtools-help] samtools 1.0 install problem Sam Nicholls
2014/08/27 Re: [Samtools-help] cram usage Praveen Raj
2014/08/27 Re: [Samtools-help] cram usage Radhouane Aniba
2014/08/27 [Samtools-help] cram usage Radhouane Aniba
2014/08/27 Re: [Samtools-help] samtools 1.0 install problem Radhouane Aniba
2014/08/27 Re: [Samtools-help] samtools 1.0 install problem Praveen Raj
2014/08/27 [Samtools-help] samtools 1.0 install problem Radhouane Aniba
2014/08/27 Re: [Samtools-help] bgzf buffering Louis Letourneau
2014/08/27 Re: [Samtools-help] An problem on replace header of bam file by using samtools Colin Hercus
2014/08/27 [Samtools-help] An problem on replace header of bam file by using samtools jiey...@annoroad.com