Questions tagged [sambamba]

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Filter bam with sambamba

I have a very large bam file and I want to filter it to keep only a handfull of positions as defined in a bed file. Can I do this with sambamba or do i need another tool? Thanks
2 votes
1 answer

Filtering paired-end reads with sambamba: avoid discarding reads on the minus strand

I have a BAM file (DNA, shallow whole genome sequencing at ~1X) where I want to filter reads (using sambamba) to keep only those which have a template length > 20 and mapping quality > 20, ...
2 votes
2 answers

BWA-mem and sambamba read group line error

this question has been asked [and answered] on Stack Overflow This is a two-part question: help interpreting an error; help with coding. I'm trying to run bwa-mem ...
1 vote
2 answers

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 from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% ...
8 votes
2 answers

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 ...
7 votes
1 answer

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 votes
2 answers

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 ...