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• • 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
  • Re: [Samtools-help] JVM crash using Picard's MarkDuplicates Louis Letourneau
• [Samtools-help] picard IlluminaBasecallstoFastq Abaan, Ogan (NIH/NCI) [E]
  • Re: [Samtools-help] picard IlluminaBasecallstoFastq Abaan, Ogan (NIH/NCI) [E]
  • Re: [Samtools-help] picard IlluminaBasecallstoFastq Nils Homer
  • Re: [Samtools-help] picard IlluminaBasecallstoFastq Lee Edsall
  • Re: [Samtools-help] picard IlluminaBasecallstoFastq Ogan ABAAN
• [Samtools-help] Manual Rieux, Adrien
  • Re: [Samtools-help] Manual John Marshall
• [Samtools-help] bcftools: invalid option -- b Todd Smith
• [Samtools-help] htslib C API km
  • Re: [Samtools-help] htslib C API Petr Danecek
• [Samtools-help] how to query a SAM/BAM file by the QNAME field? csoeder
  • Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Brent Pedersen
  • Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Charlie Soeder
  • Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? Thomas W. Blackwell
  • Re: [Samtools-help] how to query a SAM/BAM file by the QNAME field? James Nemesh
• [Samtools-help] wgsim output format document Peng Yu
• [Samtools-help] mpileup output confusion Jo R
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
  • Re: [Samtools-help] mpileup output confusion Petr Danecek
  • Re: [Samtools-help] mpileup output confusion jbr950
• [Samtools-help] samtools/bcftools/htslib 1.0 released John Marshall
• [Samtools-help] converting scaffold to bam file Khushboo Rastogi
• [Samtools-help] IO file handle support for bgzipped VCF files Jillian Rowe
  • Re: [Samtools-help] IO file handle support for bgzipped VCF files Petr Danecek
• [Samtools-help] Multi-sample variant filtering Patel, Nihir
• [Samtools-help] Picard MarkDuplicates Katherine Pillman
  • Re: [Samtools-help] Picard MarkDuplicates Alec Wysoker
• [Samtools-help] pysam - iterating over sam files without a sequence dictionary Wolfgang Maier
  • Re: [Samtools-help] pysam - iterating over sam files without a sequence dictionary Peter Cock
  • Re: [Samtools-help] pysam - iterating over sam files without a sequence dictionary Wolfgang Maier
• [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Aakriti Jain
  • Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Devon Ryan
  • Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Aakriti Jain
  • Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Devon Ryan
  • Re: [Samtools-help] Help with viewing .bam file (error: Invalid BAM binary header) Peter Cock
• [Samtools-help] htsjdk jar creation problems Mark Wadsworth
  • Re: [Samtools-help] htsjdk jar creation problems Alec Wysoker
  • Re: [Samtools-help] htsjdk jar creation problems Liu Xingliang
• [Samtools-help] multiple ALT alleles Thiago M. Venancio
  • Re: [Samtools-help] multiple ALT alleles Petr Danecek
• [Samtools-help] mpileup output Thiago M. Venancio
  • Re: [Samtools-help] mpileup output Devon Ryan
  • Re: [Samtools-help] mpileup output Thiago M. Venancio
  • Re: [Samtools-help] mpileup output Devon Ryan
  • Re: [Samtools-help] mpileup output Thiago M. Venancio
  • Re: [Samtools-help] mpileup output Devon Ryan
  • Re: [Samtools-help] mpileup output Thiago M. Venancio
• [Samtools-help] segmentation fault when running mpileup with -f Ian Fiddes
  • Re: [Samtools-help] segmentation fault when running mpileup with -f Petr Danecek
• [Samtools-help] variants in mpileup file but not in vcf file Manoharan
• [Samtools-help] Bioinformatics Authorship Misrepresentation Abhishek Narain Singh
  • Re: [Samtools-help] Bioinformatics Authorship Misrepresentation Peter Cock
  • Re: [Samtools-help] Bioinformatics Authorship Misrepresentation Abhishek Narain Singh
• [Samtools-help] incorrect SamFormatException in PicardTools ? Wolfgang Maier
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Wolfgang Maier
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Ben Bimber
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Ben Bimber
  • Re: [Samtools-help] incorrect SamFormatException in PicardTools ? Alec Wysoker
• [Samtools-help] Bug report for samtools indel genotyping Xiaobin Xing
• [Samtools-help] bedtools coverage question Lana Schaffer
• [Samtools-help] question about programming Sullivan, Catherine
  • Re: [Samtools-help] question about programming Joseph Fass
  • Re: [Samtools-help] question about programming John Marshall
  • Re: [Samtools-help] question about programming Sullivan, Catherine
• [Samtools-help] PicardTools 1.117 error after output bam/baifiles are written by ReorderSam Hazard, E. Starr
  • Re: [Samtools-help] PicardTools 1.117 error after output bam/baifiles are written by ReorderSam Alec Wysoker
• [Samtools-help] samtools pos-to-name map for faster re-sorting? Henrik Bengtsson
• Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Dan Bolser
  • Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Peter Cock
  • Re: [Samtools-help] Problem indexing BAM mapped to long chromosome John Marshall
  • Re: [Samtools-help] Problem indexing BAM mapped to long chromosome Dan Bolser
• [Samtools-help] Picard ValidateSamFile.jar error: bin field not equal to values based on alignment sticklenator
  • Re: [Samtools-help] Picard ValidateSamFile.jar error: bin field not equal to values based on alignment Alec Wysoker
• [Samtools-help] Picard out of memory when using CreateSequenceDictionary: Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit Bastian Schiffthaler
  • 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
• [Samtools-help] Problem when running Picard tools 胡义波
  • Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
  • Re: [Samtools-help] Problem when running Picard tools 胡义波
  • Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
  • Re: [Samtools-help] Problem when running Picard tools 胡义波
  • Re: [Samtools-help] Problem when running Picard tools 胡义波
  • Re: [Samtools-help] Problem when running Picard tools Alec Wysoker
• [Samtools-help] Picard MarkDuplicates READ_NAME_REGEX Exceptions Daniel Burkhardt
  • Re: [Samtools-help] Picard MarkDuplicates READ_NAME_REGEX Exceptions Alec Wysoker
• [Samtools-help] Samtools support for encrypted data files John Damm Sørensen
• [Samtools-help] How CalculateHsMetrics uses strand information from targets and baits files? Alexey Larionov
  • Re: [Samtools-help] How CalculateHsMetrics uses strand information from targets and baits files? Alec Wysoker
• [Samtools-help] CollectWgsMetrics complains about MQ=null Kanterakis, Efstathios
  • Re: [Samtools-help] CollectWgsMetrics complains about MQ=null Alec Wysoker
• [Samtools-help] Alleles counts obtained for independent samples... Rieux, Adrien
  • Re: [Samtools-help] Alleles counts obtained for independent samples... Petr Danecek
• [Samtools-help] Samtools view options not in v0.1.19? Baker, Daniel N.
  • Re: [Samtools-help] Samtools view options not in v0.1.19? Devon Ryan
  • Re: [Samtools-help] Samtools view options not in v0.1.19? Baker, Daniel N.
• [Samtools-help] Problem with complex indel CIGAR strings for SAM to BAM conversions Adam Scott
  • Re: [Samtools-help] Problem with complex indel CIGAR strings for SAM to BAM conversions Thomas W. Blackwell
• [Samtools-help] samtools for mapped reads Zhao, Shanrong
  • Re: [Samtools-help] samtools for mapped reads Colin Hercus
• [Samtools-help] Pacbio sam->bam problems James Kerwin
  • Re: [Samtools-help] Pacbio sam->bam problems Peter Cock
• [Samtools-help] BAM to faatsq Zhao, Shanrong
  • Re: [Samtools-help] BAM to faatsq Alec Wysoker
  • Re: [Samtools-help] BAM to faatsq Zhao, Shanrong
  • Re: [Samtools-help] BAM to faatsq Alec Wysoker
• [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" Christian Cole
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" Marcel Martin
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" Bob Harris
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" John Marshall
  • Re: [Samtools-help] Seeking verification of meaning of "file truncation" Marcel Martin
• [Samtools-help] (no subject) Shohini Ghosh
  • Re: [Samtools-help] (no subject) Alec Wysoker
  • Re: [Samtools-help] (no subject) Marcel Martin
  • Re: [Samtools-help] (no subject) Alec Wysoker
  • [Samtools-help] (no subject) Kevin
  • Re: [Samtools-help] unsubscribing from samtools-help John Marshall
  • Re: [Samtools-help] (no subject) Peter Cock
  • [Samtools-help] (no subject) Denis Goryunov
  • [Samtools-help] (no subject) Mónica Fabbro
  • [Samtools-help] (no subject) Robert Davies
  • [Samtools-help] (no subject) Jody Phelan
• [Samtools-help] UTR regions in CollectRNASeqMetrics Alexander Predeus
  • Re: [Samtools-help] UTR regions in CollectRNASeqMetrics Tim Fennell
• Re: [Samtools-help] Calling variants error Adrian Pelin
• [Samtools-help] unusual output from idxstats Gaidatzis, Dimosthenis
  • Re: [Samtools-help] unusual output from idxstats Peter Cock
• [Samtools-help] Fwd: Meaning of SGB Field Brett Dutro
  • Re: [Samtools-help] Fwd: Meaning of SGB Field Petr Danecek
  • Re: [Samtools-help] Fwd: Meaning of SGB Field Brett Dutro
• [Samtools-help] Picard_logging to file Eugenie Denisova
  • Re: [Samtools-help] Picard_logging to file Alec Wysoker
• [Samtools-help] samtools api to get pileup information Xiaobin Xing
• [Samtools-help] samtools -s 0.95 doesnt work.. Dror Hibsh
  • Re: [Samtools-help] samtools -s 0.95 doesnt work.. Dror Hibsh
  • Re: [Samtools-help] samtools -s 0.95 doesnt work.. Christian Cole
• [Samtools-help] PicardTools 1.96 runs on my head node but crashes on compute nodes. Hazard, E. Starr
  • Re: [Samtools-help] PicardTools 1.96 runs on my head node but crashes on compute nodes. Colin Hercus
• [Samtools-help] Some questions about "Allele frequency" in VCF file Wei-Chi Wang
• [Samtools-help] working with file with multiple primary alignments Rusch, Michael
  • Re: [Samtools-help] working with file with multiple primary alignments Alec Wysoker
  • Re: [Samtools-help] working with file with multiple primary alignme nts. . Rusch, Michael
  • Re: [Samtools-help] working with file with multiple primary alignments Colin Hercus
• [Samtools-help] Picard release 1.115 Alec Wysoker
  • Re: [Samtools-help] [Samtools-devel] Picard release 1.115 Nils Homer
  • [Samtools-help] Picard release 1.116 Alec Wysoker
  • [Samtools-help] Picard release 1.117 Alec Wysoker
  • [Samtools-help] Picard release 1.118 Alec Wysoker
• [Samtools-help] Truncated output from mpileup Scott Newman
  • Re: [Samtools-help] Truncated output from mpileup Thomas W. Blackwell
  • Re: [Samtools-help] Truncated output from mpileup Scott Newman
• [Samtools-help] broken link to specs on main samtools page Bela Tiwari
• [Samtools-help] Picard Error - "Barcode XX specified more than once" Kristian Andersen
  • Re: [Samtools-help] Picard Error - "Barcode XX specified more than once" Tim Fennell
  • Re: [Samtools-help] Picard Error - "Barcode XX specified more than once" Kristian G. Andersen
• [Samtools-help] samtools sort RAM Louis Letourneau
  • Re: [Samtools-help] samtools sort RAM Colin Hercus
  • Re: [Samtools-help] samtools sort RAM Louis Letourneau
• Re: [Samtools-help] error sam file generated from bwa mem Devon Ryan
• [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError David Langenberger
  • Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError Alec Wysoker
  • Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError David Langenberger
  • Re: [Samtools-help] Picard: EstimateLibraryComplexity -> OutOfMemoryError Alec Wysoker
• [Samtools-help] picard.sourceforge.net - explain sam flags broken Lukas Windhager
  • Re: [Samtools-help] picard.sourceforge.net - explain sam flags broken Alec Wysoker
• [Samtools-help] dual overlap Laurent MANCHON
  • Re: [Samtools-help] dual overlap Devon Ryan
• [Samtools-help] Can't manage to convert SAM to BAM Marine Rohmer
  • Re: [Samtools-help] Can't manage to convert SAM to BAM Thomas W. Blackwell
  • Re: [Samtools-help] Can't manage to convert SAM to BAM Devon Ryan
• [Samtools-help] deletion calling using samtools Wolfgang Maier
  • Re: [Samtools-help] deletion calling using samtools Wolfgang Maier
  • Re: [Samtools-help] deletion calling using samtools Joseph Fass
  • Re: [Samtools-help] deletion calling using samtools Wolfgang Maier
• [Samtools-help] strand direction carol white
  • [Samtools-help] Fw: strand direction carol white
  • Re: [Samtools-help] Fw: strand direction Wolfgang Maier
• [Samtools-help] need help to extract all the mapped reads form sorted bam file raghvendra singh
  • Re: [Samtools-help] need help to extract all the mapped reads form sorted bam file Devon Ryan
• [Samtools-help] Issues with IlluminaBasecallsToSam.jar Gire, Stephen
  • Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Alec Wysoker
  • Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Gire, Stephen
  • Re: [Samtools-help] Issues with IlluminaBasecallsToSam.jar Alec Wysoker
• [Samtools-help] align to fasta DB with names Lana Schaffer

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