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Questions tagged [bam]

The "Binary Alignment Map" (BAM) format is one of the common binary formats used to store DNA/RNA sequence alignment information. Questions should include this tag if they directly pertain to the format itself, details of BAM file usage, or errors relating to likely malformed BAM files. Also includes Sequence Alignment/Map (SAM) format, which is a human-readable version of BAM format.

SEE ALSO:
Sequence Alignment/Map Format Specification
BAM
SAM

52 questions
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snakemake: handle rule connect on wrong mode on another rule

I need to run two rules (gatk_Mutect2 and gatk_IndelRealigner) in the same snakefile. If put these rules in different snakefiles, I can run them without error. I use two input functions (get_files_somatic and get_files). Both use the case name as…
mau_who
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How to convert the large bio-format file to database-like file that can be asynchronously accessed width JavaScript

Pros! I have a visualization project that render the biological data to canvas charts, in which I use a javascritp framwork called jgv.js(the doc API) to generate canvas. Here’s a simple config demo:
1Cr18Ni9
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Bash script stops after 1 file

I'm trying to run a bioinformatics command line tool on all .bam files in a directory. This is what I'm using: #!/bin/sh reference='/path/Homo_sapiens_assembly19.fasta' for f in *.bam do base_name=${f%.bam} java -jar…
SinghG
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Create VCF from .bim, .bed and .fam files

I have a .fam, .bed and .bim file with markers for few individuals. I would need to convert it into a VCF file. Could someone help to create a VCF file. Are there any opensource tools which can do this?
chas
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Picard SamToFastq only extracts one read, then throws an error

I'm trying to extract some FastQ files from bam files. Picard can do this with SamToFastq as it says in the documentation for this tool it accepts either a bam or sam file. But when I run it, it only extracts one read, and then exits. Here is the…
Davy Kavanagh
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Perl: Create index for tab file with two columns

I have got a huge tab-seperated file with up to 200 million rows (normally around 20 million) and two columns: the first column contains an ASCII word with up to 40 chars the second contains an integer. I would like to do the following steps: sort…
Matthias Munz
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Recommended languages for reading and manipulating BAM and VCF files?

I'm normally a C# / .net developer, but a new project is going to be working with Next Generation Sequencing BAM and VCF files. I will need to read these files, make some changes, and save them. As far as I can tell, there's not much in the way of…
Kyle
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