Hello all. I am new to bioinformatics and needing some help. I have a Bam file generated from fastq, In the command I used, a sorted bam file is supposed to be created but I keep getting errors. I am trying to split the BAM file (about 50GB) into several Bam files so I can sort it separately. But I don't know how to go about this. (I am a beginner ). Any help would be appreciated, Thanks (Peter).
Question: Split BAM file.
20 months ago by
jaqx008 • 50
jaqx008 • 50 wrote:
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20 months ago by
Samarth Kulshrestha • 190
Samarth Kulshrestha • 190 wrote:
Hi, You can also explore BamTools toolkit with "split" option.
usage: bamtools [--help] COMMAND [ARGS]
Available bamtools commands:
convert Converts between BAM and a number of other formats count Prints number of alignments in BAM file(s) coverage Prints coverage statistics from the input BAM file filter Filters BAM file(s) by user-specified criteria header Prints BAM header information index Generates index for BAM file merge Merge multiple BAM files into single file random Select random alignments from existing BAM file(s), intended more as a testing tool. resolve Resolves paired-end reads (marking the IsProperPair flag as needed) revert Removes duplicate marks and restores original base qualities sort Sorts the BAM file according to some criteria ***split Splits a BAM file on user-specified property, creating a new BAM output file for each value found*** stats Prints some basic statistics from input BAM file(s)
Hope this helps.
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