samtools-help

Messages by Date

2015/05/18 [Samtools-help] Failed BAM -> CRAM -> BAM Dan Greenfield
2015/05/17 [Samtools-help] Samtools 0.1.19 RPB value help Dessislava Mladenova
2015/05/15 Re: [Samtools-help] tabix bug on cat'ed vcf.gz John Marshall
2015/05/14 [Samtools-help] inconsistent output vcf with sample number JINGJING JIN
2015/05/14 Re: [Samtools-help] tabix bug on cat'ed vcf.gz Heng Li
2015/05/14 Re: [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
2015/05/14 Re: [Samtools-help] tabix bug on cat'ed vcf.gz John Marshall
2015/05/13 Re: [Samtools-help] tabix bug on cat'ed vcf.gz Len Trigg
2015/05/13 Re: [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
2015/05/13 Re: [Samtools-help] tabix bug on cat'ed vcf.gz Peter Cock
2015/05/13 [Samtools-help] tabix bug on cat'ed vcf.gz Kanterakis, Efstathios
2015/05/13 [Samtools-help] mpileup: tradeoff between runtime and accuracy Christian Ruckert
2015/05/11 [Samtools-help] removing bad quality reads William Gilks
2015/05/08 [Samtools-help] Install Picard-1.131 without internet Zhihua Li
2015/05/08 [Samtools-help] mpileup: different number of bases and read positions when using --output-BP Carey, Lucas
2015/05/07 [Samtools-help] samtools rmdup Samuel COLLOMBET
2015/05/07 Re: [Samtools-help] Meaning of --ignore-overlaps in mpileup Wolfgang Maier
2015/05/07 [Samtools-help] mpileup segfault Sierra Love Stowell
2015/05/04 [Samtools-help] Possible Bug in CollectOxoGMetrics David Kling
2015/05/01 [Samtools-help] (no subject) Denis Goryunov
2015/04/28 Re: [Samtools-help] samtools sort crashed on 110G bam file. memory leakage? Colin Hercus
2015/04/28 Re: [Samtools-help] samtools sort crashed on 110G bam file. memory leakage? Vladimir Morozov
2015/04/27 Re: [Samtools-help] samtools sort crashed on 110G bam file. memory leakage? Colin Hercus
2015/04/27 [Samtools-help] samtools sort crashed on 110G bam file. memory leakage? Vladimir Morozov
2015/04/24 [Samtools-help] Tabix grep -c/-q equivalent? Julian Hess
2015/04/23 [Samtools-help] bcftools consensus Julian Egger
2015/04/20 [Samtools-help] allele frequency spectrum in samtools/bcftools v1.0+ Brice Sarver
2015/04/19 [Samtools-help] Error with samtools mpileup (1.2) base positions and qualities Matthew Flickinger
2015/04/17 [Samtools-help] quality scores in mpileup output Aparna
2015/04/17 [Samtools-help] .fna file extension Murphy, Terence (NIH/NLM/NCBI) [C]
2015/04/16 [Samtools-help] How to present "N" in gap region of consensus? 洪國勝
2015/04/15 Re: [Samtools-help] htsjdk unable to read CRAM files created by samtools James Bonfield
2015/04/15 [Samtools-help] htsjdk unable to read CRAM files created by samtools Þórður Kristjánsson
2015/04/14 [Samtools-help] Meaning of --ignore-overlaps in mpileup Dario Beraldi
2015/04/10 Re: [Samtools-help] Trying to run CalculateHsMetrics over a whole genome Geraldine Van der Auwera
2015/04/08 Re: [Samtools-help] samtools 1.2 - rmdup Error: bam_get_library() not yet implemented Lana Schaffer
2015/04/06 Re: [Samtools-help] samtools 1.2 - rmdup Error: bam_get_library() not yet implemented Ogan
2015/03/30 Re: [Samtools-help] orientation usage in MarkDuplicates Nils Homer
2015/03/30 Re: [Samtools-help] orientation usage in MarkDuplicates Faith Coldren
2015/03/26 Re: [Samtools-help] samtools split output filename format string error ying chen
2015/03/26 Re: [Samtools-help] samtools split output filename format string error Thomas W. Blackwell
2015/03/25 [Samtools-help] samtools split output filename format string error ying chen
2015/03/25 [Samtools-help] bcftools "Wrong number of PL fields?" error Sarah Flanagan
2015/03/23 [Samtools-help] Minimum Java Version in HTSJDK Nils Homer
2015/03/20 [Samtools-help] samtools 1.2 - rmdup Error: bam_get_library() not yet implemented Matteo Manca - Malattie Rare Sardegna
2015/03/18 Re: [Samtools-help] Per-sample consensus sequences? Thomas Sibley
2015/03/18 [Samtools-help] Per-sample consensus sequences? Thomas Sibley
2015/03/17 Re: [Samtools-help] MergeBamAlignment issue Geraldine Van der Auwera
2015/03/17 [Samtools-help] MergeBamAlignment issue Ryan Davis
2015/03/17 [Samtools-help] mpileup on a specified region with -r option : discrepancy in called variants and quality scores Kevin Dialdestoro
2015/03/16 [Samtools-help] question about bcftool merge -r ? Pengyao Jiang
2015/03/13 [Samtools-help] Samtools view over ftp without index Ogan Abaan
2015/03/12 Re: [Samtools-help] Samtools-help Digest, Vol 73, Issue 16 Geraldine Van der Auwera
2015/03/12 [Samtools-help] feature request: bamshuf switch to ignore read groups Kanterakis, Efstathios
2015/03/11 Re: [Samtools-help] samtools sort creates millions of files Bob Harris
2015/03/11 Re: [Samtools-help] samtools sort creates millions of files John Marshall
2015/03/11 Re: [Samtools-help] samtools sort creates millions of files Bob Harris
2015/03/11 Re: [Samtools-help] samtools sort creates millions of files Ashish Agarwal
2015/03/11 [Samtools-help] Samtools variant without annotation in VCF mehar
2015/03/10 Re: [Samtools-help] samtools sort creates millions of files Colin Hercus
2015/03/10 Re: [Samtools-help] samtools sort creates millions of files Monica Britton
2015/03/10 Re: [Samtools-help] samtools sort creates millions of files Ashish Agarwal
2015/03/10 Re: [Samtools-help] samtools sort creates millions of files Ashish Agarwal
2015/03/10 Re: [Samtools-help] samtools sort creates millions of files Ashish Agarwal
2015/03/10 [Samtools-help] Optical Duplicates Matt Carroll
2015/03/09 Re: [Samtools-help] samtools sort creates millions of files Thomas W. Blackwell
2015/03/09 [Samtools-help] samtools sort creates millions of files Ashish Agarwal
2015/03/09 [Samtools-help] Picard tools support is moving to the GATK support forum Geraldine Van der Auwera
2015/03/05 Re: [Samtools-help] orientation usage in MarkDuplicates Nils Homer
2015/03/05 [Samtools-help] orientation usage in MarkDuplicates Faith Coldren
2015/03/04 Re: [Samtools-help] Problem using unpaired_fastq for SamToFastq (v.1.119) Nils Homer
2015/03/02 [Samtools-help] Problem using unpaired_fastq for SamToFastq (v.1.119) Jasleen Grewal
2015/03/02 [Samtools-help] Duplicate Marking Mayra Eduardoff
2015/02/28 [Samtools-help] How to make consensus by applying multiple mapping Farzaneh Salari
2015/02/25 [Samtools-help] consensus calling over zero pileup regions Giuseppe Aprea
2015/02/23 [Samtools-help] Picard release 1.129 Jason Carey
2015/02/23 Re: [Samtools-help] Problem with samtools mpileup Peter Cock
2015/02/23 Re: [Samtools-help] documentation on CSI format John Marshall
2015/02/23 [Samtools-help] documentation on CSI format Adam Birnbaum
2015/02/23 [Samtools-help] Problem with samtools mpileup David Francisco
2015/02/19 Re: [Samtools-help] Association Test with mpileup Vincent Lacroix
2015/02/17 Re: [Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp Peter Cock
2015/02/17 Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics Trakhtenberg, Feliks
2015/02/17 Re: [Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp Stefan Nordlander
2015/02/17 Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics Nils Homer
2015/02/17 Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics Trakhtenberg, Feliks
2015/02/17 Re: [Samtools-help] CollectAlignmentSummaryMetrics - Adapter sequences incorrect use of adapter sequence parametesr? Nils Homer
2015/02/17 Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics Nils Homer
2015/02/17 Re: [Samtools-help] MarkDuplicates and Supplemental Alignments Nils Homer
2015/02/15 [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics Trakhtenberg, Feliks
2015/02/15 [Samtools-help] CollectAlignmentSummaryMetrics - Adapter sequences incorrect use of adapter sequence parametesr? Kevin Rue-Albrecht
2015/02/13 Re: [Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp Peter Cock
2015/02/13 [Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp Stefan Nordlander
2015/02/13 [Samtools-help] RE : Association Test with mpileup LACROIX VINCENT
2015/02/13 Re: [Samtools-help] canŒt set Java environment in OS X 10.2 Christian Cole (Staff)
2015/02/12 [Samtools-help] can‘t set Java environment in OS X 10.2 yoyofangliu
2015/02/12 Re: [Samtools-help] picard compatibility with samtools -u bams? John Marshall
2015/02/12 Re: [Samtools-help] picard compatibility with samtools -u bams? Heng Li
2015/02/12 Re: [Samtools-help] picard compatibility with samtools -u bams? Peter Cock
2015/02/11 [Samtools-help] HS_PENALTY_30X calculation Ducar, Matthew D.
2015/02/11 [Samtools-help] picard compatibility with samtools -u bams? Sendu Bala
2015/02/11 Re: [Samtools-help] Association Test with mpileup Heng Li
2015/02/11 Re: [Samtools-help] Samtools-help Digest, Vol 73, Issue 11 - Re: GT doubt Clarissa Boschiero
2015/02/10 [Samtools-help] using bcftools to filter REF & ALT alleles Jack Van Handenhove
2015/02/10 Re: [Samtools-help] GT doubt Thomas Keane
2015/02/10 [Samtools-help] GT doubt Clarissa Boschiero
2015/02/09 Re: [Samtools-help] Question relavent to flagstat Devon Ryan
2015/02/09 Re: [Samtools-help] Question relavent to flagstat Xiao Li
2015/02/09 Re: [Samtools-help] Question relavent to flagstat Devon Ryan
2015/02/09 [Samtools-help] Question relavent to flagstat Xiao Li
2015/02/06 [Samtools-help] MarkDuplicates and Supplemental Alignments Schlesinger, Felix
2015/02/06 [Samtools-help] samtools merge Giuseppe Aprea
2015/02/06 Re: [Samtools-help] Cant launch Samtools Wolfgang Maier
2015/02/05 Re: [Samtools-help] Cant launch Samtools Peter Cock
2015/02/05 [Samtools-help] Cant launch Samtools Νικόλαος Νικηφόρος Γιακουμάκης
2015/02/04 Re: [Samtools-help] picard reordersam Nils Homer
2015/02/04 [Samtools-help] picard reordersam Ceres Fernandez Rozadilla
2015/02/04 Re: [Samtools-help] Samtools/BCFtools/HTSlib 1.2 released Ogan
2015/02/04 [Samtools-help] Samtools/BCFtools/HTSlib 1.2 released John Marshall
2015/02/03 Re: [Samtools-help] Picard help: MarkDuplicates Nils Homer
2015/02/03 [Samtools-help] Picard help: MarkDuplicates Katie Faust Stryjewski
2015/02/03 [Samtools-help] formatting the output from bcftools 杨一子
2015/02/02 Re: [Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities) Paul Lott
2015/02/02 Re: [Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities) Petr Danecek
2015/01/31 [Samtools-help] vcfutils.pl error Bradley Wubbenhorst
2015/01/30 [Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities) Paul Lott
2015/01/29 Re: [Samtools-help] Programmatically sort and index a converted bam file Devon Ryan
2015/01/29 Re: [Samtools-help] Help Nils Homer
2015/01/29 [Samtools-help] Programmatically sort and index a converted bam file Johannes Helmuth
2015/01/28 [Samtools-help] fastq to unmapped sam Matei David
2015/01/28 [Samtools-help] Help 黄桦
2015/01/27 [Samtools-help] Multithreaded sort for samtools 1.1 Lorenzo Pesce
2015/01/27 Re: [Samtools-help] mpileup slow Alissa Severson
2015/01/27 Re: [Samtools-help] regression on picard BuildBamIndex Nils Homer
2015/01/27 Re: [Samtools-help] regression on picard BuildBamIndex Ben Bimber
2015/01/27 Re: [Samtools-help] mpileup slow Peter Cock
2015/01/27 [Samtools-help] mpileup slow Alissa Severson
2015/01/26 [Samtools-help] MarkDuplicate: NoClassDefFoundError Zhu Zhuo
2015/01/23 Re: [Samtools-help] QS field in the INFO section of VCF Petr Danecek
2015/01/22 Re: [Samtools-help] samtools [pretty_header] invalid header error, with no clue Devon Ryan
2015/01/22 [Samtools-help] samtools [pretty_header] invalid header error, with no clue Axel Rasche
2015/01/22 [Samtools-help] QS field in the INFO section of VCF David
2015/01/22 [Samtools-help] Removing redundancy in SAM format (coming from redundant input) Dan Bolser
2015/01/20 Re: [Samtools-help] regression on picard BuildBamIndex Renan Valieris
2015/01/19 Re: [Samtools-help] regression on picard BuildBamIndex Nils Homer
2015/01/19 Re: [Samtools-help] multi-threaded sort out of memory Matei David
2015/01/19 Re: [Samtools-help] multi-threaded sort out of memory Heng Li
2015/01/19 Re: [Samtools-help] multi-threaded sort out of memory Devon Ryan
2015/01/19 Re: [Samtools-help] multi-threaded sort out of memory Christian Cole (Staff)
2015/01/19 Re: [Samtools-help] samtools sort Devon Ryan
2015/01/19 [Samtools-help] multi-threaded sort out of memory Matei David
2015/01/19 [Samtools-help] regression on picard BuildBamIndex Renan Valieris
2015/01/19 [Samtools-help] samtools sort VlLADISLAV BIRYUKOV
2015/01/16 [Samtools-help] mpileup and MAPQ cutoff Emeric Dubois
2015/01/15 Re: [Samtools-help] samtools flagstat - help Anshika Srivastava
2015/01/15 [Samtools-help] samtools flagstat - help Anshika Srivastava
2015/01/14 Re: [Samtools-help] bz2 files Heng Li
2015/01/14 Re: [Samtools-help] bz2 files Magnus Manske
2015/01/14 Re: [Samtools-help] bz2 files Heng Li
2015/01/14 [Samtools-help] bz2 files Denise Mauldin
2015/01/13 [Samtools-help] adding a tools like polishbam to Picard Stephane Plaisance | VIB |
2015/01/12 [Samtools-help] Question: Samtools MPILEUP on single-end/paired-end data Christian Hinze
2015/01/08 [Samtools-help] Samtools bamshuf random or not Ogan
2014/12/24 [Samtools-help] 1.1 issue with Cufflinks Ben Ernest
2014/12/22 [Samtools-help] problem 王学强
2014/12/21 [Samtools-help] getting java.lang.OutOfMemoryError Neeraj Suthar
2014/12/21 [Samtools-help] samtools out of memory error nahal mansoury
2014/12/19 [Samtools-help] question about supplementary alignments and samtools and picard Ines Pires
2014/12/19 Re: [Samtools-help] samtools index bug with coordinates higher than 1 billion Petr Danecek
2014/12/18 Re: [Samtools-help] IlluminaBasecallsToSam Header error Nils Homer
2014/12/18 Re: [Samtools-help] Picard/CleanSam.jar dubts Nils Homer
2014/12/18 Re: [Samtools-help] RevertBam command in Picard-tools-1.126 threw exception Nils Homer
2014/12/18 Re: [Samtools-help] Picard CollectGcBiasMetrics: Exception counting mismatches Nils Homer
2014/12/18 [Samtools-help] Continuation to post Picard CollectGcBiasMetrics: Exception counting mismatches Sivakumar Gowrisankar
2014/12/18 [Samtools-help] Picard CollectGcBiasMetrics: Exception counting mismatches Sivakumar Gowrisankar
2014/12/18 Re: [Samtools-help] bcftools not in samtools 1.0 Thomas Keane
2014/12/17 Re: [Samtools-help] bcftools not in samtools 1.0 Adrian Pelin
2014/12/17 [Samtools-help] bcftools not in samtools 1.0 Lana Schaffer
2014/12/17 Re: [Samtools-help] Tabix Makefile.PL John Marshall
2014/12/17 Re: [Samtools-help] SamToFastq: found unpaired mates Ogan
2014/12/17 [Samtools-help] Tabix Makefile.PL Will McLaren
2014/12/16 Re: [Samtools-help] samtools index bug with coordinates higher than 1 billion Heng Li
2014/12/16 [Samtools-help] samtools index bug with coordinates higher than 1 billion olivier.rue
2014/12/15 [Samtools-help] Picard Release 1.127 Jason Carey
2014/12/15 [Samtools-help] Samtools merge unmapped Ogan
2014/12/11 [Samtools-help] Hom Vs Het variant calls mehar
2014/12/10 Re: [Samtools-help] maintaining read groups when merging bam files Ryan G
2014/12/10 Re: [Samtools-help] Is there a way to have the exact counts of reads (DP=sum of the 4 col of DP4) ? Petr Danecek
2014/12/09 [Samtools-help] Is there a way to have the exact counts of reads (DP=sum of the 4 col of DP4) ? Jeanne Ropars
2014/12/09 [Samtools-help] Calling Ref when no Ref base called Ryan Kevin (GUY'S AND ST THOMAS' NHS FOUNDATION TRUST)
2014/12/08 [Samtools-help] maintaining read groups when merging bam files Martin, Jessica L.
2014/12/08 Re: [Samtools-help] unsubscribing from samtools-help John Marshall
2014/12/05 Re: [Samtools-help] CollectHiSeqXPfFailMetrics Error: Could not find a format with available files for the following data types: Position Kanterakis, Efstathios
2014/12/05 Re: [Samtools-help] (no subject) Peter Cock
2014/12/05 Re: [Samtools-help] AO and RO tags Petr Danecek
2014/12/05 Re: [Samtools-help] Splitting multiallelic sites using "bcftools norm" Petr Danecek
2014/12/04 Re: [Samtools-help] AO and RO tags Adrian Pelin
2014/12/04 [Samtools-help] (no subject) Kevin
2014/12/04 Re: [Samtools-help] CollectHiSeqXPfFailMetrics Error: Could not find a format with available files for the following data types: Position Matt Sooknah
2014/12/04 Re: [Samtools-help] CollectHiSeqXPfFailMetrics Error: Could not find a format with available files for the following data types: Position Matt Sooknah