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• [Samtools-help] mpileup differences between samtools and bcftools Nate Brown
  • Re: [Samtools-help] mpileup differences between samtools and bcftools [EXT] Robert Davies
• [Samtools-help] Release 1.21 Robert Davies
• [Samtools-help] Release 1.20 Robert Davies
• [Samtools-help] SAMtools release 1.19.2 Robert Davies
• [Samtools-help] SAMtools and HTSlib release 1.19.1 Robert Davies
• [Samtools-help] Release 1.19 Robert Davies
• [Samtools-help] new user Christopher Blair
  • Re: [Samtools-help] new user Tom Blackwell
• [Samtools-help] Release 1.18 Robert Davies
• [Samtools-help] support to CRAM gzip Adrian
  • Re: [Samtools-help] support to CRAM gzip [EXT] James Bonfield
• [Samtools-help] Release 1.17 Robert Davies
• [Samtools-help] Problem with RNAME field in bam gilsanan
• [Samtools-help] Samtools installation problem Trine Riemer
• [Samtools-help] Fwd: Humble request and help_replacing variants that failed quality metrics with "N" with bcftools [EXT] Jennifer Liddle
• [Samtools-help] Question about samtools mpileup and overlapping reads Carla Mariner Llicer
  • Re: [Samtools-help] Question about samtools mpileup and overlapping reads [EXT] James Bonfield
• Re: [Samtools-help] consensus not recognized [EXT] James Bonfield
• [Samtools-help] SAMtools release 1.16.1 Robert Davies
• [Samtools-help] Release 1.16 Robert Davies
• [Samtools-help] bcftools isec retain duplicates Thomas Juettemann
  • Re: [Samtools-help] bcftools isec retain duplicates [EXT] Robert Davies
  • Re: [Samtools-help] bcftools isec retain duplicates [EXT] Thomas Juettemann
  • Re: [Samtools-help] bcftools isec retain duplicates [EXT] James Bonfield
• [Samtools-help] questions about samtools index Ruixue Liu
  • Re: [Samtools-help] questions about samtools index Peter Cock via Samtools-help
• [Samtools-help] Release 1.15.1 Robert Davies
• [Samtools-help] Release 1.15 Robert Davies
• [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Sabine van Schie
  • Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Peter Cock via Samtools-help
  • Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT] James Bonfield
  • Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Robert Davies
  • Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Sabine van Schie
  • Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT] Robert Davies
• [Samtools-help] changing the order of input changes samtools merge ouput Zhezhen Wang
  • Re: [Samtools-help] changing the order of input changes samtools merge ouput [EXT] James Bonfield
• [Samtools-help] bcftools mpileup help bparreira
  • Re: [Samtools-help] bcftools mpileup help [EXT] Petr Danecek
• [Samtools-help] Question regarding SAMtools tview alignment characters Loïc Meunier
  • Re: [Samtools-help] Question regarding SAMtools tview alignment characters [EXT] James Bonfield
• [Samtools-help] BCF tools 1.9 header order important? Thomas Juettemann
  • Re: [Samtools-help] BCF tools 1.9 header order important? [EXT] Petr Danecek
• [Samtools-help] BCF tools sort Thomas Juettemann
  • Re: [Samtools-help] BCF tools sort [EXT] James Bonfield
• [Samtools-help] Release 1.14 Robert Davies
• [Samtools-help] samtools stats - can I get base frequency based on the position in an alignment rather than original sequence position? Benjamin Franzmayr
• [Samtools-help] Samtools write files to S3 bucket Dilkash Ghazala
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
  • Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
• Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1 Stéphane Plaisance
  • Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1 Dr . Frank Vorhölter
• [Samtools-help] samtools depth multi-threading option Dr . Frank Vorhölter
• [Samtools-help] Different coverage between weeSAM and samtools mpileup result Ching Ching WEE
  • Re: [Samtools-help] Different coverage between weeSAM and samtools mpileup result [EXT] James Bonfield
• [Samtools-help] Release 1.13 Robert Davies
• [Samtools-help] Samtools Reheader help request Marsha Wallace
  • Re: [Samtools-help] Samtools Reheader help request [EXT] Valeriu Ohan
  • Re: [Samtools-help] Samtools Reheader help request [EXT] Marsha Wallace
• [Samtools-help] SAM tag for polyA sites Kodali, Vamsi (NIH/NLM/NCBI) [C] via Samtools-help
• [Samtools-help] Release 1.12 Robert Davies
• [Samtools-help] fail to read header in v1.10, v1.11 Remik Ziemlinski
  • Re: [Samtools-help] fail to read header in v1.10, v1.11 John Marshall
  • Re: [Samtools-help] fail to read header in v1.10, v1.11 [EXT] James Bonfield
• [Samtools-help] samtools mpileup --no-BAQ Shadrina, Mariya
• [Samtools-help] generating headers Baiba Alksere
  • Re: [Samtools-help] generating headers [EXT] Valeriu Ohan
• [Samtools-help] tabix and bgzip Baiba Alksere
  • Re: [Samtools-help] tabix and bgzip [EXT] Andrew Whitwham
• [Samtools-help] samtools view -L vs location args Keiran Raine
  • Re: [Samtools-help] samtools view -L vs location args [EXT] Valeriu Ohan
  • Re: [Samtools-help] samtools view -L vs location args [EXT] Keiran Raine
• [Samtools-help] Release 1.11 Robert Davies
  • Re: [Samtools-help] Release 1.11 Elisabeth Diatta via Samtools-help
  • Re: [Samtools-help] Release 1.11 [EXT] Petr Danecek
  • Re: [Samtools-help] Release 1.11 [EXT] Elisabeth Diatta via Samtools-help
  • Re: [Samtools-help] Release 1.11 [EXT] Petr Danecek
  • Re: [Samtools-help] Release 1.11 [EXT] Elisabeth Diatta via Samtools-help
• [Samtools-help] Filter on integer tags not working Benjamin Audit
  • Re: [Samtools-help] Filter on integer tags not working [EXT] Robert Davies
• [Samtools-help] problems with header Baiba Alksere
  • Re: [Samtools-help] problems with header [EXT] Andrew Whitwham
• [Samtools-help] Bcftools call -G Pooja Singh
  • Re: [Samtools-help] Bcftools call -G [EXT] Petr Danecek
• [Samtools-help] samtools stats Nadia Baig
  • Re: [Samtools-help] samtools stats [EXT] Andrew Whitwham
  • Re: [Samtools-help] samtools stats [EXT] Nadia Baig
  • Re: [Samtools-help] samtools stats [EXT] Andrew Whitwham
  • Re: [Samtools-help] samtools stats [EXT] Nadia Baig
• [Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error White, Noor (NIH/NEI) [F] via Samtools-help
  • Re: [Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error [EXT] Petr Danecek
• [Samtools-help] Extracting region as fasta John Crow
  • Re: [Samtools-help] Extracting region as fasta Thomas W. Blackwell
  • Re: [Samtools-help] Extracting region as fasta Colin
• [Samtools-help] --write-index - csi? Keiran Raine
  • Re: [Samtools-help] --write-index - csi? Nowoshilow,Sergej
  • Re: [Samtools-help] --write-index - csi? [EXT] Keiran Raine
  • Re: [Samtools-help] --write-index - csi? [EXT] Nowoshilow,Sergej
  • Re: [Samtools-help] --write-index - csi? [EXT] Keiran Raine
• [Samtools-help] markdup "-c" option Keiran Raine
  • Re: [Samtools-help] markdup "-c" option [EXT] aw7
  • Re: [Samtools-help] markdup "-c" option [EXT] Keiran Raine
• [Samtools-help] Samtools collate - location of temporary files Keiran Raine
  • Re: [Samtools-help] Samtools collate - location of temporary files John Marshall
  • Re: [Samtools-help] Samtools collate - location of temporary files [EXT] Keiran Raine
• [Samtools-help] samtools sort command results in symbols calculation Pedro Hollanda Carvalho
  • Re: [Samtools-help] samtools sort command results in symbols calculation John Marshall
• [Samtools-help] SAM to BAM permission denied Pedro Hollanda Carvalho
  • Re: [Samtools-help] SAM to BAM permission denied [EXT] Robert Davies
• [Samtools-help] read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag Justin Jeyakani
  • Re: [Samtools-help] read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag [EXT] Valeriu Ohan
• [Samtools-help] How to include original base quality from FASTQ file into (OQ) existing bam file Justin Jeyakani
• [Samtools-help] Samtools markdup vs picard markduplicates Jon Belton
  • Re: [Samtools-help] Samtools markdup vs picard markduplicates Andrew Whitwham
• [Samtools-help] The order of @SQ lines defines the alignment sorting order Richard Wilton
  • Re: [Samtools-help] The order of @SQ lines defines the alignment sorting order [EXT] James Bonfield
• [Samtools-help] Release 1.10 Robert Davies
• [Samtools-help] Question about SGB Carrasco Valenzuela, Tomas
• [Samtools-help] Compiling samtools or htslib with MPI? Is it possible? Darin Lory
• [Samtools-help] reset sam/bam/cram iterator Brent Pedersen
• [Samtools-help] inconsistency in samtools mpilup basequality Karina Borlaug
  • Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] James Bonfield
  • Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Karina Borlaug
  • Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Robert Davies
  • Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Karina Borlaug
• Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] Chris Norman
• [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? Colin
  • Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? Colin
  • Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] James Bonfield
  • Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] Colin
  • Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] James Bonfield
• [Samtools-help] Index format issue Bai, Bing
• [Samtools-help] effect of capping read mapping qualities Wolfgang Maier
• [Samtools-help] samtools not working with BWA -C flag Aengus Stewart
  • Re: [Samtools-help] samtools not working with BWA -C flag Robert Davies
  • Re: [Samtools-help] samtools not working with BWA -C flag Thomas W. Blackwell
  • Re: [Samtools-help] samtools not working with BWA -C flag Aengus Stewart
  • Re: [Samtools-help] samtools not working with BWA -C flag John Marshall
  • Re: [Samtools-help] samtools not working with BWA -C flag Jennifer Liddle
• [Samtools-help] Regarding error in SNP calling Ankita Mishra
• [Samtools-help] Calculating abundance of reads Renuka Agarwal
• [Samtools-help] Regarding consensus file Renuka Agarwal
  • Re: [Samtools-help] Regarding consensus file Petr Danecek
  • Re: [Samtools-help] Regarding consensus file [EXT] Petr Danecek
  • [Samtools-help] Regarding consensus file Renuka Agarwal
• [Samtools-help] Regarding samtools and bcftools commands Renuka Agarwal
  • Re: [Samtools-help] Regarding samtools and bcftools commands Thomas W. Blackwell
• [Samtools-help] Question re BAM to CRAM James Jacobs
  • Re: [Samtools-help] Question re BAM to CRAM Peter Cock via Samtools-help
• [Samtools-help] Reading files from private S3 bucket Rob Thompson
  • Re: [Samtools-help] Reading files from private S3 bucket John Marshall
• [Samtools-help] samtools view -T option Alexander Brown
  • Re: [Samtools-help] samtools view -T option James Bonfield
  • Re: [Samtools-help] samtools view -T option Thomas W. Blackwell
• [Samtools-help] Binary files generated on Windows Remik Ziemlinski
  • Re: [Samtools-help] Binary files generated on Windows Robert Davies
  • Re: [Samtools-help] Binary files generated on Windows Remik Ziemlinski
  • Re: [Samtools-help] Binary files generated on Windows Robert Davies
• [Samtools-help] Help splitting a bam file to facilitating sorting Yarza, Fauna
  • Re: [Samtools-help] Help splitting a bam file to facilitating sorting James Bonfield
  • Re: [Samtools-help] Help splitting a bam file to facilitating sorting Sam Nicholls
  • Re: [Samtools-help] Help splitting a bam file to facilitating sorting Nowoshilow,Sergej
  • Re: [Samtools-help] Help splitting a bam file to facilitating sorting Yarza, Fauna
• [Samtools-help] writing BAM and SAM files Will Stokes
  • Re: [Samtools-help] writing BAM and SAM files James Bonfield
  • Re: [Samtools-help] writing BAM and SAM files Will Stokes
  • Re: [Samtools-help] writing BAM and SAM files James Bonfield
  • Re: [Samtools-help] writing BAM and SAM files Will Stokes
  • Re: [Samtools-help] writing BAM and SAM files James Bonfield
  • Re: [Samtools-help] writing BAM and SAM files Will Stokes
  • Re: [Samtools-help] writing BAM and SAM files James Bonfield
  • Re: [Samtools-help] writing BAM and SAM files Will Stokes
  • [Samtools-help] writing BAM and SAM files Will Stokes
• [Samtools-help] read sequence Brent Pedersen
  • Re: [Samtools-help] read sequence James Bonfield
  • Re: [Samtools-help] read sequence Brent Pedersen
• [Samtools-help] result from samtools mpileup LH LV
• [Samtools-help] bcftools mpileup baq options? Sendu Bala
  • Re: [Samtools-help] bcftools mpileup baq options? Petr Danecek
• [Samtools-help] how to get list chrom from a bcf file ? sebastien letort
  • Re: [Samtools-help] how to get list chrom from a bcf file ? Braulio Valdebenito Maturana
  • Re: [Samtools-help] how to get list chrom from a bcf file ? sebastien letort
  • Re: [Samtools-help] how to get list chrom from a bcf file ? Petr Danecek
• [Samtools-help] Samtools FASTQ unexpected output Kost, Jason
  • Re: [Samtools-help] Samtools FASTQ unexpected output Kost, Jason
• Re: [Samtools-help] Command not found Robert Davies
• [Samtools-help] Installing Samtools Michael Bunnemeyer
• [Samtools-help] merging vcf files Sandip Kale
• [Samtools-help] [W::sam_parse1] urecognized reference name Nowoshilow,Sergej
  • Re: [Samtools-help] [W::sam_parse1] urecognized reference name Robert Davies
• [Samtools-help] Reference used for alignment vs CRAM compression Ziga Mahkovec
  • Re: [Samtools-help] Reference used for alignment vs CRAM compression Thomas W. Blackwell
  • Re: [Samtools-help] Reference used for alignment vs CRAM compression James Bonfield
  • Re: [Samtools-help] Reference used for alignment vs CRAM compression Ziga Mahkovec
• [Samtools-help] Release 1.9 Robert Davies
• [Samtools-help] per-file depth in samtools mpileup Jing meng

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