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Samtools failed to read header

WebFeb 19, 2024 · The text was updated successfully, but these errors were encountered: WebJun 17, 2024 · The most common samtools view filtering options are: -q N – only report alignment records with mapping quality of at least N ( >= N ). -f 0xXX – only report alignment records where the specified flags are all set (are all 1) you can provide the flags in decimal, or as here as hexadecimal. -F 0xXX – only report alignment records where the ...

samtools view: writing to standard output failed: Broken pipe

WebMar 23, 2024 · The problem is that without an input file, samtools sort tries to read from stdin. Using a recent samtools, you can however coordinate sort the SAM and write a … http://www.htslib.org/doc/samtools-reheader.html thomas josef schmitz https://wildlifeshowroom.com

samtools sort [bam_merge_core] [bam_sort_core] errors?

WebJun 7, 2011 · Try truncating the file to see if it's a filesystem issue (assuming it's a 64-bit system?): head -100000 outX300.sam > test100k.sam samtools view -bS -o test100k.bam test100k.sam 2. Try simply moving the file elsewhere and trying again? 3. Try Version: 0.1.7 ? WebMar 23, 2024 · The problem is that without an input file, samtools sort tries to read from stdin. Using a recent samtools, you can however coordinate sort the SAM and write a sorted BAM using: samtools sort -o "$ {baseName}.bam" "mapped_$ {baseName}.sam" WebJul 8, 2024 · Update: it's good to know that the samtools / bcftools pipelines are at least producing consistent results, which suggests that the error is not associated with the output format on the mpileup side of the pipeline, and also good to see that you've identified that this was a memory issue. uhaul moundsville wv

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Category:samtools-reheader(1) manual page

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Samtools failed to read header

samtools-reheader(1) manual page

WebMay 25, 2024 · mdehoon commented on May 25, 2024. That's because samtools now rejects completely empty files, on the assumption that they were made by an upstream process that failed rather than deliberately. … WebInclude the header in the output. -H, --header-only Output the header only. --no-header When producing SAM format, output alignment records but not headers. This is the default; the …

Samtools failed to read header

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WebOct 13, 2024 · The stack trace does not specify which GVCF file has the GZIP header issue, so it could be any of those files. In order to solve the issue, try these steps: Re-generate the indexes for all of the .vcf.gz files that are input to VariantRecalibrator. If step #1 does not solve the problem, re-run VariantRecalibrator removing each GVCF input ...

WebMar 16, 2024 · Most ERRORs can typically be fixed using Picard tools to either correct the formatting or fill in missing information, although sometimes you may want to simply filter out malformed reads using Samtools. For example, MISSING_READ_GROUP errors can be solved by adding the read group information to your data using the AddOrReplaceGroups … WebJun 7, 2011 · Try truncating the file to see if it's a filesystem issue (assuming it's a 64-bit system?): head -100000 outX300.sam > test100k.sam samtools view -bS -o test100k.bam …

WebSep 14, 2024 · You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length … WebAug 12, 2012 · I think that samtools 0.1.18 will still abort with an error if it runs across a sequence name that is not in the header. For example, I ran the following on a well-formed bam file: samtools view input.bam samtools view -bS - [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!

WebOct 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:

WebAug 3, 2024 · The samtools error is likely because it is receiving no output from the bwa mem command. Try running the bwa mem command by itself, and see if it returns a … thomas joseph azzarello floridahttp://www.htslib.org/doc/samtools-view.html thomas joseph abbertonWebsamtools 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 header in in.header.sam . This command is much faster than replacing the header with a BAM→SAM→BAM conversion. thomas joseph answers today