Questions tagged [sambamba]

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Mapping statistics from bam file using bbtools and sambamba

Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% ...
8
votes
2answers
421 views

Convert bam file to highly compressible bam

I have a large collection of bam files and I want to post-process each of them into another bam where I can make queries about: the reads position and pair-endness, insert sizes, MAPQ and other ...
6
votes
1answer
447 views

low-memory high-speed replacement for Picard MarkDuplicates

I am running Picard MarkDuplicates with the following parameters below. On the file described, it takes about 41.6Gb of RAM memory and about 20-25 minutes to compute (only uses 1 core AFAICS). ...
9
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2answers
4k views

samtools depth print out all positions

I am trying to use samtools depth (v1.4) with the -a option and a bed file listing the human chromosomes chr1-chr22, chrX, chrY, and chrM to print out the coverage ...