Samtools reheader example

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August undefined, 2024

WebAug 20, 2014 · Multi-sample and multiplexed example Suppose that you have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp … WebApr 11, 2024 · I am getting error while using samtools reheader. my command is: path/to/samtools reheader -i HG100.sam > HG100.bam I got following error both the times. [E::hts_open] fail to open file '-i' [main_reheader] fail to read the header from -i. HG100.sam is 4.9GB Following shows it's header details:

samtools reheader cannot replace header in-place #1604

Websamtools-reheader. This tool replaces the header in the input file. This tool provides speed, the traditional way to change up headers is to go from BAM file to SAM, change the … WebDESCRIPTION. Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, … dishes look white agter washing

Running GATK DepthOfCoverage on BAM files with multiple RG

Websamtools reheader – replaces the header in the input file SYNOPSIS. samtools reheader [-iP] [-c CMD in.header.sam] in.bam. DESCRIPTION. Replace the header in in.bam with the … WebNov 20, 2013 · The samtools help To bring up the help, just type samtools As you can see, there are multiple “subcommands” and for samtools to work you must tell it which … http://www.htslib.org/doc/1.13/samtools-reheader.html dishes like chicken piccata

samtools/samtools-reheader – BioLib

WebAnyway, the quickest way to do what you want is to samtools view -H foo.bam > header to get the BAM header and then change each NCBI "chromosome name" to its corresponding UCSC chromosome name. DO NOT REORDER THE LINES! You can then use samtools reheader and be done. WebThe samtools-1.10.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files. Changes affecting the whole of samtools, or multiple sub-commands: Samtools now uses the new HTSlib header API. dishes look sweaty in dishwasherWebNov 20, 2013 · Our goal is to work through examples that demonstrate how to explore, process and manipulate SAM and BAM files with the samtools software package. For future reference, use the samtools documentation. Installing samtools Follow these steps: dishes low in saturated fat

"WebFeb 22, 2011 · It adds the (possibly ill-conceived) @CO record. Cliff needs either to add @RG records somewhere along the line before calling MarkDuplicates using Picard ReplaceSamHeader or Samtools reheader. Ideally the thing to do would be to add them before merging, and then use Picard's MergeSamFiles instead of samtools to merge. " - Samtools reheader example

samtools reheader cannot replace header in-place #1604

Running GATK DepthOfCoverage on BAM files with multiple RG

Samtools reheader example

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