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Results tagged with samtools
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user 1770
Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
5
votes
3
answers
566
views
Is there an efficient way to check an input BAM in R?
Perhaps pipe to samtools (which doesn't feel very stable in terms of software)? …
- 1,423
2
votes
1
answer
153
views
SAM format: Does the BAM "Integer or numeric array" field no longer exist? Why?
+ Integer or numeric array
However, looking at the samtools source code, I noticed this:
https://github.com/samtools/samtools/blob/develop/sam_view.c#L920-L931
switch (aux_type) {
case 'H': … Was this the case with previous versions of samtools? …
- 1,423
7
votes
2
answers
704
views
How does htslib/samtools access optional BAM fields?
My questions:
How does htslib/samtools (e.g. samtools view) access these optional fields, which differ in number from BAM to BAM (possible row to row)? … When a user runs htslib or even samtools view, how does the BAM row "end", i.e. what data structure exists to show that the BAM row has no more optional fields, and that the algorithm should "move on" …
- 1,423
6
votes
5
answers
4k
views
Subset smaller BAM to contain several thousand rows from multiple chromosomes
Normally I do the following, which will subset the BAM file.bam and keep the header
samtools view -H file.bam > header.sam
samtools view file.bam | head -n 5000 | cat header.sam - | samtools view -Sb … samtools view file.bam | grep "chr1" | cat header.sam - | samtools view -Sb - > file.unique.bam
but then I have two problems:
(1) I may not be grepping the alignments to chromsome 2---there may exist …
- 1,423
2
votes
1
answer
1k
views
Modifying a SAM header after removing all non-primary reads
I subset a BAM to only include primary reads using the following samtools commands:
samtools view -F 256 input.bam > input.primaryOnly.sam
Now, in order to convert this SAM into a new subsetted BAM, … view -H input.bam > input.header.sam
Then I could convert the SAM into a BAM with
samtools view -S -b i new.sam > new.bam
My problem is, I'm using the original BAM header. …
- 1,423
3
votes
1
answer
509
views
What is the standard way to measure contig sequence lengths in a BAM?
My understanding is that the community would use samtools idxstats to compute this information from the corresponding index file.
Are there more precise/standard approaches? …
- 1,423
8
votes
7
answers
13k
views
How to subset a BAM by a list of QNAMEs?
Naturally, I can do this individually, e.g.
samtools view file.bam | grep 'EXAMPLE:QNAME1' > subset.bam
But I'm unsure how to do this for a list of QNAMES:
How do I write a for loop that will do all …
- 1,423
7
votes
1
answer
2k
views
How to remove all BAM read groups from all reads (not just the header)?
Normally when I have such a problem, I remove all the read groups from the BAM header as follows:
samtools view -H your.bam | grep -v "^@RG" | samtools reheader - original.bam > new.bam
and then I would …
- 1,423