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12 votes

Convert bam file to highly compressible bam

You can just set the fields you don't need to *: ...
Devon Ryan's user avatar
  • 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. ...
morgantaschuk's user avatar
4 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
Clarus Salvus's user avatar
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?" ...
Pierre's user avatar
  • 1,536
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 ...
Devon Ryan's user avatar
  • 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 ...
gringer's user avatar
  • 14.3k
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 ...
Einar's user avatar
  • 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 ...
John Marshall's user avatar
1 vote

Filter bam with sambamba

I think it is possible: sambamba view --regions regions.bed --with-header --format=bam reads.bam > filtered.bam
Pablo's user avatar
  • 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....
Timur Shtatland's user avatar

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