samtools-help

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2024/10/30 Re: [Samtools-help] mpileup differences between samtools and bcftools [EXT] Robert Davies
2024/10/21 [Samtools-help] mpileup differences between samtools and bcftools Nate Brown
2024/09/12 [Samtools-help] Release 1.21 Robert Davies
2024/04/15 [Samtools-help] Release 1.20 Robert Davies
2024/01/24 [Samtools-help] SAMtools release 1.19.2 Robert Davies
2024/01/22 [Samtools-help] SAMtools and HTSlib release 1.19.1 Robert Davies
2023/12/12 [Samtools-help] Release 1.19 Robert Davies
2023/10/24 Re: [Samtools-help] new user Tom Blackwell
2023/10/24 [Samtools-help] new user Christopher Blair
2023/07/25 [Samtools-help] Release 1.18 Robert Davies
2023/07/05 Re: [Samtools-help] support to CRAM gzip [EXT] James Bonfield
2023/07/05 [Samtools-help] support to CRAM gzip Adrian
2023/02/21 [Samtools-help] Release 1.17 Robert Davies
2022/11/29 [Samtools-help] Problem with RNAME field in bam gilsanan
2022/11/09 [Samtools-help] Samtools installation problem Trine Riemer
2022/11/02 [Samtools-help] Fwd: Humble request and help_replacing variants that failed quality metrics with "N" with bcftools [EXT] Jennifer Liddle
2022/10/25 Re: [Samtools-help] Question about samtools mpileup and overlapping reads [EXT] James Bonfield
2022/10/25 [Samtools-help] Question about samtools mpileup and overlapping reads Carla Mariner Llicer
2022/09/08 Re: [Samtools-help] consensus not recognized [EXT] James Bonfield
2022/09/02 [Samtools-help] SAMtools release 1.16.1 Robert Davies
2022/08/18 [Samtools-help] Release 1.16 Robert Davies
2022/08/04 Re: [Samtools-help] bcftools isec retain duplicates [EXT] James Bonfield
2022/08/04 Re: [Samtools-help] bcftools isec retain duplicates [EXT] Thomas Juettemann
2022/08/03 Re: [Samtools-help] bcftools isec retain duplicates [EXT] Robert Davies
2022/08/02 [Samtools-help] bcftools isec retain duplicates Thomas Juettemann
2022/04/22 Re: [Samtools-help] questions about samtools index Peter Cock via Samtools-help
2022/04/20 [Samtools-help] questions about samtools index Ruixue Liu
2022/04/07 [Samtools-help] Release 1.15.1 Robert Davies
2022/02/21 [Samtools-help] Release 1.15 Robert Davies
2022/01/19 Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT] Robert Davies
2022/01/19 Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Sabine van Schie
2022/01/18 Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Robert Davies
2022/01/18 Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice [EXT] James Bonfield
2022/01/18 Re: [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Peter Cock via Samtools-help
2022/01/18 [Samtools-help] Issue with cram file indexing, reference sequence MD5 mismatch for slice Sabine van Schie
2022/01/13 Re: [Samtools-help] changing the order of input changes samtools merge ouput [EXT] James Bonfield
2022/01/13 [Samtools-help] changing the order of input changes samtools merge ouput Zhezhen Wang
2022/01/05 Re: [Samtools-help] bcftools mpileup help [EXT] Petr Danecek
2022/01/04 [Samtools-help] bcftools mpileup help bparreira
2022/01/04 Re: [Samtools-help] Question regarding SAMtools tview alignment characters [EXT] James Bonfield
2021/12/21 [Samtools-help] Question regarding SAMtools tview alignment characters Loïc Meunier
2021/11/29 Re: [Samtools-help] BCF tools 1.9 header order important? [EXT] Petr Danecek
2021/11/29 [Samtools-help] BCF tools 1.9 header order important? Thomas Juettemann
2021/11/09 Re: [Samtools-help] BCF tools sort [EXT] James Bonfield
2021/11/08 [Samtools-help] BCF tools sort Thomas Juettemann
2021/10/22 [Samtools-help] Release 1.14 Robert Davies
2021/09/24 [Samtools-help] samtools stats - can I get base frequency based on the position in an alignment rather than original sequence position? Benjamin Franzmayr
2021/09/16 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
2021/09/14 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
2021/09/14 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
2021/09/14 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
2021/09/14 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Dilkash Ghazala
2021/09/14 Re: [Samtools-help] Samtools write files to S3 bucket [EXT] Andrew Whitwham
2021/09/13 [Samtools-help] Samtools write files to S3 bucket Dilkash Ghazala
2021/08/25 Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1 Dr . Frank Vorhölter
2021/08/25 Re: [Samtools-help] Samtools-help Digest, Vol 140, Issue 1 Stéphane Plaisance
2021/08/24 [Samtools-help] samtools depth multi-threading option Dr . Frank Vorhölter
2021/07/26 Re: [Samtools-help] Different coverage between weeSAM and samtools mpileup result [EXT] James Bonfield
2021/07/23 [Samtools-help] Different coverage between weeSAM and samtools mpileup result Ching Ching WEE
2021/07/09 [Samtools-help] Release 1.13 Robert Davies
2021/06/22 Re: [Samtools-help] Samtools Reheader help request [EXT] Marsha Wallace
2021/06/22 Re: [Samtools-help] Samtools Reheader help request [EXT] Valeriu Ohan
2021/06/17 [Samtools-help] Samtools Reheader help request Marsha Wallace
2021/04/16 [Samtools-help] SAM tag for polyA sites Kodali, Vamsi (NIH/NLM/NCBI) [C] via Samtools-help
2021/03/17 [Samtools-help] Release 1.12 Robert Davies
2021/03/11 Re: [Samtools-help] fail to read header in v1.10, v1.11 [EXT] James Bonfield
2021/03/11 Re: [Samtools-help] fail to read header in v1.10, v1.11 John Marshall
2021/03/11 [Samtools-help] fail to read header in v1.10, v1.11 Remik Ziemlinski
2020/11/11 [Samtools-help] samtools mpileup --no-BAQ Shadrina, Mariya
2020/10/28 Re: [Samtools-help] generating headers [EXT] Valeriu Ohan
2020/10/27 [Samtools-help] generating headers Baiba Alksere
2020/10/12 Re: [Samtools-help] tabix and bgzip [EXT] Andrew Whitwham
2020/10/12 [Samtools-help] tabix and bgzip Baiba Alksere
2020/09/24 Re: [Samtools-help] Release 1.11 [EXT] Elisabeth Diatta via Samtools-help
2020/09/24 Re: [Samtools-help] samtools view -L vs location args [EXT] Keiran Raine
2020/09/24 Re: [Samtools-help] samtools view -L vs location args [EXT] Valeriu Ohan
2020/09/24 [Samtools-help] samtools view -L vs location args Keiran Raine
2020/09/24 Re: [Samtools-help] Release 1.11 [EXT] Petr Danecek
2020/09/23 Re: [Samtools-help] Release 1.11 [EXT] Elisabeth Diatta via Samtools-help
2020/09/22 Re: [Samtools-help] Release 1.11 [EXT] Petr Danecek
2020/09/22 Re: [Samtools-help] Release 1.11 Elisabeth Diatta via Samtools-help
2020/09/22 [Samtools-help] Release 1.11 Robert Davies
2020/09/11 Re: [Samtools-help] Filter on integer tags not working [EXT] Robert Davies
2020/09/11 [Samtools-help] Filter on integer tags not working Benjamin Audit
2020/09/02 Re: [Samtools-help] problems with header [EXT] Andrew Whitwham
2020/09/02 [Samtools-help] problems with header Baiba Alksere
2020/08/13 Re: [Samtools-help] Bcftools call -G [EXT] Petr Danecek
2020/08/13 [Samtools-help] Bcftools call -G Pooja Singh
2020/07/16 Re: [Samtools-help] samtools stats [EXT] Nadia Baig
2020/07/16 Re: [Samtools-help] samtools stats [EXT] Andrew Whitwham
2020/07/16 Re: [Samtools-help] samtools stats [EXT] Nadia Baig
2020/07/16 Re: [Samtools-help] samtools stats [EXT] Andrew Whitwham
2020/07/16 [Samtools-help] samtools stats Nadia Baig
2020/07/06 Re: [Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error [EXT] Petr Danecek
2020/07/05 [Samtools-help] "Use of uninitialized value $l in numeric lt (<)" Error White, Noor (NIH/NEI) [F] via Samtools-help
2020/06/19 Re: [Samtools-help] Extracting region as fasta Colin
2020/06/19 Re: [Samtools-help] Extracting region as fasta Thomas W. Blackwell
2020/06/18 [Samtools-help] Extracting region as fasta John Crow
2020/06/13 Re: [Samtools-help] --write-index - csi? Nowoshilow,Sergej
2020/06/13 Re: [Samtools-help] --write-index - csi? [EXT] Keiran Raine
2020/06/13 Re: [Samtools-help] --write-index - csi? [EXT] Nowoshilow,Sergej
2020/06/13 Re: [Samtools-help] --write-index - csi? [EXT] Keiran Raine
2020/06/13 [Samtools-help] --write-index - csi? Keiran Raine
2020/06/12 Re: [Samtools-help] markdup "-c" option [EXT] Keiran Raine
2020/06/12 Re: [Samtools-help] markdup "-c" option [EXT] aw7
2020/06/12 [Samtools-help] markdup "-c" option Keiran Raine
2020/06/08 Re: [Samtools-help] Samtools collate - location of temporary files [EXT] Keiran Raine
2020/06/08 Re: [Samtools-help] Samtools collate - location of temporary files John Marshall
2020/06/08 [Samtools-help] Samtools collate - location of temporary files Keiran Raine
2020/04/23 Re: [Samtools-help] samtools sort command results in symbols calculation John Marshall
2020/04/22 [Samtools-help] samtools sort command results in symbols calculation Pedro Hollanda Carvalho
2020/04/20 Re: [Samtools-help] read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag [EXT] Valeriu Ohan
2020/04/20 Re: [Samtools-help] SAM to BAM permission denied [EXT] Robert Davies
2020/04/20 [Samtools-help] SAM to BAM permission denied Pedro Hollanda Carvalho
2020/04/20 [Samtools-help] read and write a bam: but duplicate the quality column (11) and write one with "OQ:Z:" flag Justin Jeyakani
2020/04/11 [Samtools-help] How to include original base quality from FASTQ file into (OQ) existing bam file Justin Jeyakani
2020/03/04 Re: [Samtools-help] Samtools markdup vs picard markduplicates Andrew Whitwham
2020/03/03 [Samtools-help] Samtools markdup vs picard markduplicates Jon Belton
2020/02/27 Re: [Samtools-help] The order of @SQ lines defines the alignment sorting order [EXT] James Bonfield
2020/02/26 [Samtools-help] The order of @SQ lines defines the alignment sorting order Richard Wilton
2019/12/06 [Samtools-help] Release 1.10 Robert Davies
2019/07/25 [Samtools-help] Question about SGB Carrasco Valenzuela, Tomas
2019/07/01 [Samtools-help] Compiling samtools or htslib with MPI? Is it possible? Darin Lory
2019/06/26 [Samtools-help] reset sam/bam/cram iterator Brent Pedersen
2019/06/17 Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Karina Borlaug
2019/06/17 Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Robert Davies
2019/06/17 Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] Karina Borlaug
2019/06/17 Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT] James Bonfield
2019/06/14 [Samtools-help] inconsistency in samtools mpilup basequality Karina Borlaug
2019/06/04 Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] Chris Norman
2019/06/03 Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] James Bonfield
2019/05/30 Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] Colin
2019/05/30 Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? [EXT] James Bonfield
2019/05/22 Re: [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? Colin
2019/05/22 [Samtools-help] Usage of the 'b' item in CRAM format (with MarkDuplicates)? Colin
2019/05/07 [Samtools-help] Index format issue Bai, Bing
2019/03/25 [Samtools-help] effect of capping read mapping qualities Wolfgang Maier
2019/03/14 Re: [Samtools-help] samtools not working with BWA -C flag Jennifer Liddle
2019/03/14 Re: [Samtools-help] samtools not working with BWA -C flag John Marshall
2019/03/14 Re: [Samtools-help] samtools not working with BWA -C flag Aengus Stewart
2019/03/14 Re: [Samtools-help] samtools not working with BWA -C flag Thomas W. Blackwell
2019/03/14 Re: [Samtools-help] samtools not working with BWA -C flag Robert Davies
2019/03/14 [Samtools-help] samtools not working with BWA -C flag Aengus Stewart
2019/02/23 [Samtools-help] Regarding consensus file Renuka Agarwal
2019/02/20 [Samtools-help] Regarding error in SNP calling Ankita Mishra
2019/02/18 [Samtools-help] Calculating abundance of reads Renuka Agarwal
2019/02/14 Re: [Samtools-help] Regarding consensus file [EXT] Petr Danecek
2019/02/12 Re: [Samtools-help] Regarding consensus file Petr Danecek
2019/02/11 [Samtools-help] Regarding consensus file Renuka Agarwal
2019/02/08 Re: [Samtools-help] Regarding samtools and bcftools commands Thomas W. Blackwell
2019/02/07 [Samtools-help] Regarding samtools and bcftools commands Renuka Agarwal
2019/01/24 Re: [Samtools-help] Question re BAM to CRAM Peter Cock via Samtools-help
2019/01/23 [Samtools-help] Question re BAM to CRAM James Jacobs
2018/12/19 Re: [Samtools-help] Reading files from private S3 bucket John Marshall
2018/12/17 [Samtools-help] Reading files from private S3 bucket Rob Thompson
2018/11/28 Re: [Samtools-help] samtools view -T option Thomas W. Blackwell
2018/11/28 Re: [Samtools-help] samtools view -T option James Bonfield
2018/11/27 [Samtools-help] samtools view -T option Alexander Brown
2018/11/19 Re: [Samtools-help] writing BAM and SAM files Will Stokes
2018/11/16 Re: [Samtools-help] writing BAM and SAM files James Bonfield
2018/11/09 Re: [Samtools-help] writing BAM and SAM files Will Stokes
2018/11/07 Re: [Samtools-help] writing BAM and SAM files James Bonfield
2018/11/06 Re: [Samtools-help] writing BAM and SAM files Will Stokes
2018/11/06 Re: [Samtools-help] writing BAM and SAM files James Bonfield
2018/11/05 Re: [Samtools-help] writing BAM and SAM files Will Stokes
2018/11/05 Re: [Samtools-help] Binary files generated on Windows Robert Davies
2018/11/02 Re: [Samtools-help] Binary files generated on Windows Remik Ziemlinski
2018/11/02 Re: [Samtools-help] Binary files generated on Windows Robert Davies
2018/11/02 [Samtools-help] Binary files generated on Windows Remik Ziemlinski
2018/11/01 Re: [Samtools-help] read sequence Brent Pedersen
2018/11/01 Re: [Samtools-help] Help splitting a bam file to facilitating sorting Yarza, Fauna
2018/11/01 Re: [Samtools-help] Help splitting a bam file to facilitating sorting Sam Nicholls
2018/11/01 Re: [Samtools-help] Help splitting a bam file to facilitating sorting James Bonfield
2018/10/31 Re: [Samtools-help] Help splitting a bam file to facilitating sorting Nowoshilow,Sergej
2018/10/31 [Samtools-help] Help splitting a bam file to facilitating sorting Yarza, Fauna
2018/10/30 Re: [Samtools-help] writing BAM and SAM files James Bonfield
2018/10/29 [Samtools-help] writing BAM and SAM files Will Stokes
2018/10/29 [Samtools-help] writing BAM and SAM files Will Stokes
2018/10/22 Re: [Samtools-help] read sequence James Bonfield
2018/10/19 [Samtools-help] read sequence Brent Pedersen
2018/10/17 Re: [Samtools-help] bcftools mpileup baq options? Petr Danecek
2018/10/17 Re: [Samtools-help] how to get list chrom from a bcf file ? Petr Danecek
2018/09/26 [Samtools-help] result from samtools mpileup LH LV
2018/09/24 [Samtools-help] bcftools mpileup baq options? Sendu Bala
2018/09/18 Re: [Samtools-help] how to get list chrom from a bcf file ? sebastien letort
2018/09/18 Re: [Samtools-help] how to get list chrom from a bcf file ? Braulio Valdebenito Maturana
2018/09/18 [Samtools-help] how to get list chrom from a bcf file ? sebastien letort
2018/09/08 Re: [Samtools-help] REF_CACHE Brent Pedersen
2018/08/28 Re: [Samtools-help] Samtools FASTQ unexpected output Kost, Jason
2018/08/28 [Samtools-help] Samtools FASTQ unexpected output Kost, Jason
2018/08/28 Re: [Samtools-help] Command not found Robert Davies
2018/08/24 [Samtools-help] Installing Samtools Michael Bunnemeyer
2018/08/14 [Samtools-help] merging vcf files Sandip Kale
2018/08/13 Re: [Samtools-help] [W::sam_parse1] urecognized reference name Robert Davies
2018/08/12 [Samtools-help] [W::sam_parse1] urecognized reference name Nowoshilow,Sergej
2018/08/03 Re: [Samtools-help] Reference used for alignment vs CRAM compression Ziga Mahkovec
2018/08/03 Re: [Samtools-help] Reference used for alignment vs CRAM compression James Bonfield
2018/08/02 Re: [Samtools-help] Reference used for alignment vs CRAM compression Thomas W. Blackwell
2018/08/02 [Samtools-help] Reference used for alignment vs CRAM compression Ziga Mahkovec
2018/07/18 [Samtools-help] Release 1.9 Robert Davies

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