12
votes
Convert bam file to highly compressible bam
You can just set the fields you don't need to *:
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- 19.6k
6
votes
Accepted
samtools depth print out all positions
You might try using bedtools genomecov instead. If you provide the -d option, it reports the coverage at every position in the BAM file.
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- 540
3
votes
BWA-mem and sambamba read group line error
Read groups must start with RG, that is a hardcoded requirement of the SAM format, nothing you can do about that.
See https://samtools.github.io/hts-specs/SAMv1.pdf
3
votes
Convert bam file to highly compressible bam
I wrote http://lindenb.github.io/jvarkit/Biostar173114.html for biostars "What is the best way to make a bam file smaller by removing unwanted information?"
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- 1,501
2
votes
low-memory high-speed replacement for Picard MarkDuplicates
As you suggested, sambamba is faster at marking duplicates than picard (it's also multithreaded). Recent versions of samtools have a rewritten duplicate marking algorithm, though I doubt it'll be as ...
- 19.6k
2
votes
samtools depth print out all positions
Just replace the -a option with -aa:
samtools depth -b $bedfile -aa $inputfile
I see that ...
- 13.8k
1
vote
Accepted
Filtering paired-end reads with sambamba: avoid discarding reads on the minus strand
The reason is that sambamba does not use the absolute value of the template length, so, if the read maps so the minus strand, the template length is actually ...
- 131
1
vote
BWA-mem and sambamba read group line error
My sequences were generated with an MGI sequencer and the readgroups are identified like this @S200031047L1C001R0020000243/1
Those are MGI read names, not read ...
- 956
1
vote
Filter bam with sambamba
I think it is possible:
sambamba view --regions regions.bed --with-header --format=bam reads.bam > filtered.bam
- 121
1
vote
Accepted
Mapping statistics from bam file using bbtools and sambamba
Try samtools flagstat or sambamba flagstat to get similar type of information about your bam file. It may be easier to interpret....
- 839
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