Messages by Thread
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[Samtools-help] samtools sort crashed on 110G bam file. memory leakage?
Vladimir Morozov
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[Samtools-help] Tabix grep -c/-q equivalent?
Julian Hess
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[Samtools-help] bcftools consensus
Julian Egger
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[Samtools-help] allele frequency spectrum in samtools/bcftools v1.0+
Brice Sarver
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[Samtools-help] Error with samtools mpileup (1.2) base positions and qualities
Matthew Flickinger
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[Samtools-help] quality scores in mpileup output
Aparna
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[Samtools-help] .fna file extension
Murphy, Terence (NIH/NLM/NCBI) [C]
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[Samtools-help] How to present "N" in gap region of consensus?
洪 國勝
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[Samtools-help] htsjdk unable to read CRAM files created by samtools
Þórður Kristjánsson
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[Samtools-help] Meaning of --ignore-overlaps in mpileup
Dario Beraldi
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Re: [Samtools-help] Trying to run CalculateHsMetrics over a whole genome
Geraldine Van der Auwera
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[Samtools-help] bcftools "Wrong number of PL fields?" error
Sarah Flanagan
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[Samtools-help] Minimum Java Version in HTSJDK
Nils Homer
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[Samtools-help] samtools 1.2 - rmdup Error: bam_get_library() not yet implemented
Matteo Manca - Malattie Rare Sardegna
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[Samtools-help] Per-sample consensus sequences?
Thomas Sibley
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[Samtools-help] MergeBamAlignment issue
Ryan Davis
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[Samtools-help] mpileup on a specified region with -r option : discrepancy in called variants and quality scores
Kevin Dialdestoro
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[Samtools-help] question about bcftool merge -r ?
Pengyao Jiang
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[Samtools-help] Samtools view over ftp without index
Ogan Abaan
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Re: [Samtools-help] Samtools-help Digest, Vol 73, Issue 16
Geraldine Van der Auwera
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[Samtools-help] feature request: bamshuf switch to ignore read groups
Kanterakis, Efstathios
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[Samtools-help] Samtools variant without annotation in VCF
mehar
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[Samtools-help] Optical Duplicates
Matt Carroll
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[Samtools-help] samtools sort creates millions of files
Ashish Agarwal
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[Samtools-help] Picard tools support is moving to the GATK support forum
Geraldine Van der Auwera
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[Samtools-help] orientation usage in MarkDuplicates
Faith Coldren
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[Samtools-help] Problem using unpaired_fastq for SamToFastq (v.1.119)
Jasleen Grewal
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[Samtools-help] Duplicate Marking
Mayra Eduardoff
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[Samtools-help] How to make consensus by applying multiple mapping
Farzaneh Salari
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[Samtools-help] consensus calling over zero pileup regions
Giuseppe Aprea
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[Samtools-help] Picard release 1.129
Jason Carey
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[Samtools-help] documentation on CSI format
Adam Birnbaum
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[Samtools-help] Problem with samtools mpileup
David Francisco
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[Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's CollectRnaSeqMetrics
Trakhtenberg, Feliks
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[Samtools-help] CollectAlignmentSummaryMetrics - Adapter sequences incorrect use of adapter sequence parametesr?
Kevin Rue-Albrecht
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[Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp
Stefan Nordlander
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Re: [Samtools-help] canŒt set Java environment in OS X 10.2
Christian Cole (Staff)
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[Samtools-help] can‘t set Java environment in OS X 10.2
yoyofangliu
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[Samtools-help] HS_PENALTY_30X calculation
Ducar, Matthew D.
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[Samtools-help] picard compatibility with samtools -u bams?
Sendu Bala
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Re: [Samtools-help] Association Test with mpileup
Heng Li
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Re: [Samtools-help] Samtools-help Digest, Vol 73, Issue 11 - Re: GT doubt
Clarissa Boschiero
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[Samtools-help] using bcftools to filter REF & ALT alleles
Jack Van Handenhove
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[Samtools-help] GT doubt
Clarissa Boschiero
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[Samtools-help] Question relavent to flagstat
Xiao Li
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[Samtools-help] MarkDuplicates and Supplemental Alignments
Schlesinger, Felix
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[Samtools-help] samtools merge
Giuseppe Aprea
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[Samtools-help] Cant launch Samtools
Νικόλαος Νικηφόρος Γιακουμάκης
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[Samtools-help] picard reordersam
Ceres Fernandez Rozadilla
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[Samtools-help] Samtools/BCFtools/HTSlib 1.2 released
John Marshall
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[Samtools-help] Picard help: MarkDuplicates
Katie Faust Stryjewski
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[Samtools-help] formatting the output from bcftools
杨一子
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[Samtools-help] vcfutils.pl error
Bradley Wubbenhorst
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[Samtools-help] samtools mpileup v1.1 output significantly different from 0.1.19 (starting in middle of base qualities)
Paul Lott
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[Samtools-help] Programmatically sort and index a converted bam file
Johannes Helmuth
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[Samtools-help] fastq to unmapped sam
Matei David
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[Samtools-help] Multithreaded sort for samtools 1.1
Lorenzo Pesce
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[Samtools-help] mpileup slow
Alissa Severson
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[Samtools-help] MarkDuplicate: NoClassDefFoundError
Zhu Zhuo
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[Samtools-help] samtools [pretty_header] invalid header error, with no clue
Axel Rasche
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[Samtools-help] QS field in the INFO section of VCF
David
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[Samtools-help] Removing redundancy in SAM format (coming from redundant input)
Dan Bolser
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[Samtools-help] multi-threaded sort out of memory
Matei David
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[Samtools-help] regression on picard BuildBamIndex
Renan Valieris
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[Samtools-help] mpileup and MAPQ cutoff
Emeric Dubois
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[Samtools-help] samtools flagstat - help
Anshika Srivastava
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[Samtools-help] bz2 files
Denise Mauldin
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[Samtools-help] adding a tools like polishbam to Picard
Stephane Plaisance | VIB |
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[Samtools-help] Question: Samtools MPILEUP on single-end/paired-end data
Christian Hinze
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[Samtools-help] Samtools bamshuf random or not
Ogan
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[Samtools-help] 1.1 issue with Cufflinks
Ben Ernest
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[Samtools-help] getting java.lang.OutOfMemoryError
Neeraj Suthar
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[Samtools-help] samtools out of memory error
nahal mansoury
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[Samtools-help] question about supplementary alignments and samtools and picard
Ines Pires
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[Samtools-help] Continuation to post Picard CollectGcBiasMetrics: Exception counting mismatches
Sivakumar Gowrisankar
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[Samtools-help] Picard CollectGcBiasMetrics: Exception counting mismatches
Sivakumar Gowrisankar
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[Samtools-help] bcftools not in samtools 1.0
Lana Schaffer
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[Samtools-help] Tabix Makefile.PL
Will McLaren
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[Samtools-help] samtools index bug with coordinates higher than 1 billion
olivier.rue
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[Samtools-help] Picard Release 1.127
Jason Carey
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[Samtools-help] Samtools merge unmapped
Ogan
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[Samtools-help] Hom Vs Het variant calls
mehar
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[Samtools-help] Is there a way to have the exact counts of reads (DP=sum of the 4 col of DP4) ?
Jeanne Ropars
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[Samtools-help] Calling Ref when no Ref base called
Ryan Kevin (GUY'S AND ST THOMAS' NHS FOUNDATION TRUST)
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[Samtools-help] maintaining read groups when merging bam files
Martin, Jessica L.
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Re: [Samtools-help] AO and RO tags
Adrian Pelin
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[Samtools-help] RNEXT,PNEXT unmapped read
Louis Letourneau
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[Samtools-help] GCoverhead limit exceeded
Sander van der Zeeuw
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[Samtools-help] Splitting multiallelic sites using "bcftools norm"
Rasmus Borup Hansen
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[Samtools-help] Better management of exit code in samtools
Radhouane Aniba
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[Samtools-help] Bcftools vcf2sex best practice
Fengyuan Hu
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[Samtools-help] CollectHiSeqXPfFailMetrics Error: Could not find a format with available files for the following data types: Position
Kanterakis, Efstathios
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[Samtools-help] "samtools cat" with one input file
Dario Beraldi
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[Samtools-help] RevertBam command in Picard-tools-1.126 threw exception
Qingguo Wang
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[Samtools-help] Null pointer exception in CreateSequenceDictionary.jar from picard-tools
L Rutter