samtools-help

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2014/08/26 [Samtools-help] samtools/bcftools strange (error ?) lack of call Mathieu Bourgey
2014/08/26 Re: [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
2014/08/26 Re: [Samtools-help] Trouble indexing a very large VCF file Tim Fennell
2014/08/25 Re: [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
2014/08/25 Re: [Samtools-help] Trouble indexing a very large VCF file Laura Clarke
2014/08/25 [Samtools-help] Picard release 1.119 Bradley Taylor
2014/08/25 [Samtools-help] Trouble indexing a very large VCF file Richard Hayes
2014/08/22 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/22 Re: [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? James Nemesh
2014/08/22 Re: [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? Jim Robinson
2014/08/22 [Samtools-help] Is this a bug in implementation, or my misunderstanding of the spec? James Nemesh
2014/08/22 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Mark Ebbert
2014/08/22 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Louis Letourneau
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Mark Ebbert
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Bob Handsaker
2014/08/21 [Samtools-help] Picard-Removing Duplicates Ankur Naqib
2014/08/21 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Nils Homer
2014/08/20 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/20 Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/20 [Samtools-help] SAMFormatException: "...bin field of BAM record does not equal value computed based on alignment start and end..." Mark Ebbert
2014/08/20 [Samtools-help] JVM crash using Picard's MarkDuplicates Thomas Sibley
2014/08/20 Re: [Samtools-help] Manual John Marshall
2014/08/19 Re: [Samtools-help] picard IlluminaBasecallstoFastq Ogan ABAAN
2014/08/19 Re: [Samtools-help] picard IlluminaBasecallstoFastq Lee Edsall
2014/08/19 Re: [Samtools-help] picard IlluminaBasecallstoFastq Nils Homer
2014/08/19 Re: [Samtools-help] picard IlluminaBasecallstoFastq Abaan, Ogan (NIH/NCI) [E]
2014/08/19 [Samtools-help] picard IlluminaBasecallstoFastq Abaan, Ogan (NIH/NCI) [E]
2014/08/19 [Samtools-help] Manual Rieux, Adrien
2014/08/18 [Samtools-help] bcftools: invalid option -- b Todd Smith
2014/08/18 [Samtools-help] htslib C API km
2014/08/18 Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? James Nemesh
2014/08/18 Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Charlie Soeder
2014/08/18 Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Thomas W. Blackwell
2014/08/18 Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Brent Pedersen
2014/08/18 [Samtools-help] how to query a SAM/BAM file by the QNAME field? csoeder
2014/08/17 [Samtools-help] wgsim output format document Peng Yu
2014/08/16 [Samtools-help] mpileup output confusion Jo R
2014/08/15 [Samtools-help] samtools/bcftools/htslib 1.0 released John Marshall
2014/08/15 [Samtools-help] converting scaffold to bam file Khushboo Rastogi
2014/08/12 [Samtools-help] IO file handle support for bgzipped VCF files Jillian Rowe
2014/08/11 [Samtools-help] Multi-sample variant filtering Patel, Nihir
2014/08/07 Re: [Samtools-help] Picard MarkDuplicates Alec Wysoker
2014/08/07 [Samtools-help] Picard MarkDuplicates Katherine Pillman
2014/08/06 Re: [Samtools-help] pysam - iterating over sam files without a sequence dictionary Wolfgang Maier
2014/08/06 Re: [Samtools-help] pysam - iterating over sam files without a sequence dictionary Peter Cock
2014/08/06 [Samtools-help] pysam - iterating over sam files without a sequence dictionary Wolfgang Maier
2014/08/06 Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Peter Cock
2014/08/06 Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Devon Ryan
2014/08/06 Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Aakriti Jain
2014/08/06 Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Devon Ryan
2014/08/06 [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Aakriti Jain
2014/08/05 Re: [Samtools-help] htsjdk jar creation problems Liu Xingliang
2014/08/05 Re: [Samtools-help] htsjdk jar creation problems Alec Wysoker
2014/08/05 [Samtools-help] htsjdk jar creation problems Mark Wadsworth
2014/08/05 [Samtools-help] multiple ALT alleles Thiago M. Venancio
2014/08/04 Re: [Samtools-help] mpileup output Thiago M. Venancio
2014/08/04 Re: [Samtools-help] mpileup output Devon Ryan
2014/08/04 Re: [Samtools-help] mpileup output Thiago M. Venancio
2014/08/04 Re: [Samtools-help] mpileup output Devon Ryan
2014/08/04 Re: [Samtools-help] mpileup output Thiago M. Venancio
2014/08/04 Re: [Samtools-help] mpileup output Devon Ryan
2014/08/04 [Samtools-help] mpileup output Thiago M. Venancio
2014/08/03 [Samtools-help] segmentation fault when running mpileup with -f Ian Fiddes
2014/08/02 Re: [Samtools-help] Bioinformatics Authorship Misrepresentation Abhishek Narain Singh
2014/08/02 Re: [Samtools-help] Bioinformatics Authorship Misrepresentation Peter Cock
2014/08/02 [Samtools-help] variants in mpileup file but not in vcf file Manoharan
2014/08/01 [Samtools-help] Bioinformatics Authorship Misrepresentation Abhishek Narain Singh
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Ben Bimber
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Ben Bimber
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Wolfgang Maier
2014/07/31 Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
2014/07/31 [Samtools-help] incorrect SamFormatException in PicardTools ? Wolfgang Maier
2014/07/30 [Samtools-help] Bug report for samtools indel genotyping Xiaobin Xing
2014/07/30 [Samtools-help] bedtools coverage question Lana Schaffer
2014/07/30 Re: [Samtools-help] question about programming Sullivan, Catherine
2014/07/30 Re: [Samtools-help] question about programming John Marshall
2014/07/29 Re: [Samtools-help] question about programming Joseph Fass
2014/07/29 [Samtools-help] question about programming Sullivan, Catherine
2014/07/28 Re: [Samtools-help] PicardTools 1.117 error after output bam/baifiles are written by ReorderSam Alec Wysoker
2014/07/28 [Samtools-help] Picard release 1.118 Alec Wysoker
2014/07/28 Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
2014/07/26 [Samtools-help] PicardTools 1.117 error after output bam/baifiles are written by ReorderSam Hazard, E. Starr
2014/07/24 [Samtools-help] samtools pos-to-name map for faster re-sorting? Henrik Bengtsson
2014/07/23 Re: [Samtools-help] Problem when running Picard tools 胡义波
2014/07/23 Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Dan Bolser
2014/07/23 Re: [Samtools-help] Problem indexing BAM mapped to long chromosome John Marshall
2014/07/23 Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Peter Cock
2014/07/23 Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Dan Bolser
2014/07/21 Re: [Samtools-help] Picard ValidateSamFile.jar error: bin field not equal to values based on alignment Alec Wysoker
2014/07/21 Re: [Samtools-help] Picard out of memory when using CreateSequenceDictionary: Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Alec Wysoker
2014/07/21 [Samtools-help] Picard ValidateSamFile.jar error: bin field not equal to values based on alignment sticklenator
2014/07/21 [Samtools-help] Picard out of memory when using CreateSequenceDictionary: Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Bastian Schiffthaler
2014/07/17 Re: [Samtools-help] Problem when running Picard tools 胡义波
2014/07/17 Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
2014/07/17 Re: [Samtools-help] Problem when running Picard tools 胡义波
2014/07/17 Re: [Samtools-help] Alleles counts obtained for independent samples... Petr Danecek
2014/07/17 Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
2014/07/17 [Samtools-help] Problem when running Picard tools 胡义波
2014/07/16 Re: [Samtools-help] Picard MarkDuplicates READ_NAME_REGEX Exceptions Alec Wysoker
2014/07/16 [Samtools-help] Picard MarkDuplicates READ_NAME_REGEX Exceptions Daniel Burkhardt
2014/07/16 [Samtools-help] Samtools support for encrypted data files John Damm Sørensen
2014/07/14 Re: [Samtools-help] How CalculateHsMetrics uses strand information from targets and baits files? Alec Wysoker
2014/07/14 [Samtools-help] How CalculateHsMetrics uses strand information from targets and baits files? Alexey Larionov
2014/07/14 Re: [Samtools-help] CollectWgsMetrics complains about MQ=null Alec Wysoker
2014/07/14 [Samtools-help] Picard release 1.117 Alec Wysoker
2014/07/11 [Samtools-help] CollectWgsMetrics complains about MQ=null Kanterakis, Efstathios
2014/07/10 [Samtools-help] Alleles counts obtained for independent samples... Rieux, Adrien
2014/07/04 Re: [Samtools-help] Samtools view options not in v0.1.19? Baker, Daniel N.
2014/07/04 Re: [Samtools-help] Samtools view options not in v0.1.19? Devon Ryan
2014/07/04 [Samtools-help] Samtools view options not in v0.1.19? Baker, Daniel N.
2014/07/03 Re: [Samtools-help] (no subject) Alec Wysoker
2014/07/03 Re: [Samtools-help] BAM to faatsq Alec Wysoker
2014/07/03 Re: [Samtools-help] Problem with complex indel CIGAR strings for SAM to BAM conversions Thomas W. Blackwell
2014/07/03 [Samtools-help] Problem with complex indel CIGAR strings for SAM to BAM conversions Adam Scott
2014/07/02 Re: [Samtools-help] samtools for mapped reads Colin Hercus
2014/07/02 [Samtools-help] samtools for mapped reads Zhao, Shanrong
2014/07/02 Re: [Samtools-help] BAM to faatsq Zhao, Shanrong
2014/07/02 Re: [Samtools-help] Pacbio sam->bam problems Peter Cock
2014/07/02 Re: [Samtools-help] Seeking verification of meaning of "file truncation" Marcel Martin
2014/07/02 Re: [Samtools-help] BAM to faatsq Alec Wysoker
2014/07/02 Re: [Samtools-help] Seeking verification of meaning of "file truncation" John Marshall
2014/07/02 [Samtools-help] Pacbio sam->bam problems James Kerwin
2014/07/02 [Samtools-help] BAM to faatsq Zhao, Shanrong
2014/07/01 Re: [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
2014/07/01 Re: [Samtools-help] Seeking verification of meaning of "file truncation" Marcel Martin
2014/07/01 Re: [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
2014/07/01 Re: [Samtools-help] Seeking verification of meaning of "file truncation" Christian Cole
2014/06/30 Re: [Samtools-help] (no subject) Marcel Martin
2014/06/30 Re: [Samtools-help] (no subject) Alec Wysoker
2014/06/30 Re: [Samtools-help] Fwd: Meaning of SGB Field Brett Dutro
2014/06/30 [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
2014/06/30 [Samtools-help] Picard release 1.116 Alec Wysoker
2014/06/30 [Samtools-help] (no subject) Shohini Ghosh
2014/06/30 Re: [Samtools-help] UTR regions in CollectRNASeqMetrics Tim Fennell
2014/06/30 Re: [Samtools-help] Fwd: Meaning of SGB Field Petr Danecek
2014/06/29 [Samtools-help] UTR regions in CollectRNASeqMetrics Alexander Predeus
2014/06/26 Re: [Samtools-help] Calling variants error Adrian Pelin
2014/06/25 Re: [Samtools-help] unusual output from idxstats Peter Cock
2014/06/25 [Samtools-help] unusual output from idxstats Gaidatzis, Dimosthenis
2014/06/23 Re: [Samtools-help] samtools -s 0.95 doesnt work.. Christian Cole
2014/06/23 Re: [Samtools-help] Picard_logging to file Alec Wysoker
2014/06/23 [Samtools-help] Fwd: Meaning of SGB Field Brett Dutro
2014/06/23 [Samtools-help] Picard_logging to file Eugenie Denisova
2014/06/23 [Samtools-help] samtools api to get pileup information Xiaobin Xing
2014/06/21 Re: [Samtools-help] samtools -s 0.95 doesnt work.. Dror Hibsh
2014/06/21 [Samtools-help] samtools -s 0.95 doesnt work.. Dror Hibsh
2014/06/18 Re: [Samtools-help] PicardTools 1.96 runs on my head node but crashes on compute nodes. Colin Hercus
2014/06/18 [Samtools-help] PicardTools 1.96 runs on my head node but crashes on compute nodes. Hazard, E. Starr
2014/06/18 Re: [Samtools-help] Truncated output from mpileup Scott Newman
2014/06/18 Re: [Samtools-help] Truncated output from mpileup Thomas W. Blackwell
2014/06/18 [Samtools-help] Some questions about "Allele frequency" in VCF file Wei-Chi Wang
2014/06/17 Re: [Samtools-help] working with file with multiple primary alignme nts. . Rusch, Michael
2014/06/16 Re: [Samtools-help] working with file with multiple primary alignments Colin Hercus
2014/06/16 Re: [Samtools-help] working with file with multiple primary alignments Alec Wysoker
2014/06/16 [Samtools-help] working with file with multiple primary alignments Rusch, Michael
2014/06/16 Re: [Samtools-help] [Samtools-devel] Picard release 1.115 Nils Homer
2014/06/16 [Samtools-help] Picard release 1.115 Alec Wysoker
2014/06/16 Re: [Samtools-help] Picard Error - "Barcode XX specified more than once" Kristian G. Andersen
2014/06/16 Re: [Samtools-help] Picard Error - "Barcode XX specified more than once" Tim Fennell
2014/06/16 [Samtools-help] Truncated output from mpileup Scott Newman
2014/06/16 [Samtools-help] broken link to specs on main samtools page Bela Tiwari
2014/06/15 [Samtools-help] Picard Error - "Barcode XX specified more than once" Kristian Andersen
2014/06/12 Re: [Samtools-help] samtools sort RAM Louis Letourneau
2014/06/12 Re: [Samtools-help] samtools sort RAM Colin Hercus
2014/06/11 [Samtools-help] samtools sort RAM Louis Letourneau
2014/06/10 Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError Alec Wysoker
2014/06/10 Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError David Langenberger
2014/06/09 Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError Alec Wysoker
2014/06/09 Re: [Samtools-help] picard.sourceforge.net - explain sam flags broken Alec Wysoker
2014/06/06 Re: [Samtools-help] error sam file generated from bwa mem Devon Ryan
2014/06/05 [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError David Langenberger
2014/06/05 [Samtools-help] picard.sourceforge.net - explain sam flags broken Lukas Windhager
2014/06/04 Re: [Samtools-help] dual overlap Devon Ryan
2014/06/04 [Samtools-help] dual overlap Laurent MANCHON
2014/06/04 Re: [Samtools-help] Can't manage to convert SAM to BAM Devon Ryan
2014/06/04 Re: [Samtools-help] Can't manage to convert SAM to BAM Thomas W. Blackwell
2014/06/04 [Samtools-help] Can't manage to convert SAM to BAM Marine Rohmer
2014/06/03 Re: [Samtools-help] deletion calling using samtools Wolfgang Maier
2014/06/03 Re: [Samtools-help] deletion calling using samtools Joseph Fass
2014/06/03 Re: [Samtools-help] deletion calling using samtools Wolfgang Maier
2014/06/02 [Samtools-help] deletion calling using samtools Wolfgang Maier
2014/06/02 Re: [Samtools-help] Fw: strand direction Wolfgang Maier
2014/06/01 [Samtools-help] Fw: strand direction carol white
2014/06/01 [Samtools-help] strand direction carol white
2014/05/29 Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Alec Wysoker
2014/05/29 Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Gire, Stephen
2014/05/29 Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Alec Wysoker
2014/05/28 Re: [Samtools-help] need help to extract all the mapped reads form sorted bam file Devon Ryan
2014/05/28 [Samtools-help] need help to extract all the mapped reads form sorted bam file raghvendra singh
2014/05/28 [Samtools-help] Issues with IlluminaBasecallsToSam.jar Gire, Stephen
2014/05/27 Re: [Samtools-help] align to fasta DB with names Thomas W. Blackwell
2014/05/27 Re: [Samtools-help] align to fasta DB with names Lana Schaffer