Samtools reheader example
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, … http://quinlanlab.org/tutorials/samtools/samtools.html
Samtools reheader example
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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. WebCare should be taken to ensure the command is quoted correctly to avoid unwanted shell expansions (for example of $ variables). CMD must return an exit status of zero. EXAMPLES o Remove comment lines samtools reheader -c 'grep -v ^@CO' in.bam o Add "Chr" prefix to chromosome names. Note extra backslashes before dollar signs to prevent unwanted ...
WebSep 6, 2024 · Samtools gives "truncated file" when trying to view a "reheaded" file. I have a BAM file that works fine, but after using samtools reheader, I cannot view it in samtools. The new file has the same size as the original. I run the command: samtools reheader -P header.sam input.bam > output.bam. WebExamples >>> from Bio.Sequencing.Applications import BwaIndexCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> index_cmd = BwaIndexCommandline ... Command line wrapper for samtools reheader. Replace the header in in.bam with the header in in.header.sam, equivalent to:
WebNov 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: http://quinlanlab.org/tutorials/samtools/samtools.html
WebAug 19, 2024 · there is no option -sample so your command is interpreted as -s ample, however the failure was not checked there are no FORMAT fields in your VCF, therefore it makes no sense to add samples gzipped files are not supported by reheader, you'll need to convert to plain VCF, BCF, or BGZF-compressed VCF or BCF.
WebExamples Remove comment lines samtools reheader -c 'grep -v ^@CO' in.bam Add “Chr” prefix to chromosome names. Note extra backslashes before dollar signs to prevent … how can i get a non molestation orderWebCare should be taken to ensure the command is quoted correctly to avoid unwanted shell expansions (for example of $ variables). CMD must return an exit status of zero. … how can i get an order of protection nycWebAug 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 … how can i get an offshore bank accountWebOct 6, 2010 · You may try "samtools merge", using options -r and -h. You write your @RG header lines in a file provided to -h; -r will add RG:Z: tag to each of the alignment, based on file names. EDIT: for an example: http://sourceforge.net/apps/mediawik...rged_alignment In this wike, one can found the following commands: how many people can go in a black cabhttp://www.htslib.org/doc/1.13/samtools-reheader.html how can i get an original death certificateWebSamtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions … how can i get another email addressWebThe following are 30 code examples of subprocess.call () . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module subprocess , or try the search function . Example #1 how can i get an owners manual for my car