User: jkbonfield
jkbonfield • 400
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Posts by jkbonfield
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... Samtools depth is using the mpileup algorithm to find overlapping data, along with all the nuances that involves. That means filtering by flags (unmapped data, secondary reads, duplicates, QC failure), limits of maximum depth, possibly some other things like removal of overlapping templates (I can ...
written 4 months ago by
jkbonfield • 400
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... The answer about sizes has already been given so I won't repeat it.
However in answer to part 2, we locally use Biobambam's bamseqchksum tool to validate that a file operation hasn't lost data in the process, or that it's lost only the bits we know will be lost. For example it can compute checksum ...
written 5 months ago by
jkbonfield • 400
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... This sounds much like the ReducedReads format from early GATK versions. Ultimately it was retired because it wasn't sufficient to capture all the important information, but it may still be available if you can find an old enough GATK (2.8?). ...
written 5 months ago by
jkbonfield • 400
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Comment:
C: BAM files compression
... I did the maths on how long it takes to recover AWS CPU costs (based on a spot price some arbitrary time ago) in the reduction of AWS standard S3 disk charges for a BAM to CRAM conversion. At that point it happened to be around 1 day! Obviously longer for cheaper storage tiers.
I didn't do the r ...
written 6 months ago by
jkbonfield • 400
• updated
6 months ago by
RamRS ♦ 28k
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Answer:
C: BAM files compression
... CRAM generation is actually faster than BAM generation in samtools, at least at the default compression levels. CRAM decoding is slower than BAM though unless you're I/O bound, in which case CRAM will be faster due to being smaller.
See https://github.com/samtools/www.htslib.org/pull/23/commits/6a ...
written 6 months ago by
jkbonfield • 400
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... `Bcftools mpileup` should be used instead of `samtools mpileup` for variant calling. That is, the VCF / BCF output mode of mpileup is better in bcftools.
`Samtools mpileup` however has two different formats with the default always being a simple columnar format showing chr, pos, reference, depth, ...
written 6 months ago by
jkbonfield • 400
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... If you think you'll be doing markdup at some point then you may also want to add a "samtools fixmate -m" in there after the bowtie command as this way it doesn't require an additional sort later on. Also when piping it's often best to pipe uncompressed BAM. Some samtools commands have a "-u" optio ...
written 6 months ago by
jkbonfield • 400
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... Samtools markdup is written to match Picard 2.10.3 (also Biobambam's bamstreamingmarkduplicates) so if you can find documentation on those then it should also apply to Samtools.
It may seem like a complex dance to have both name and position sorted requirements, but this is perhaps due to a traditi ...
written 6 months ago by
jkbonfield • 400
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... Not an answer as I haven't implemented this myself so don't know all the ins and outs.
However basically the BAI index maps ranges (produced as "bins") to file offsets. Given the R-Tree isn't binary, a single bin may have multiple start/stop points for data within it, hence the linear index too.
...
written 7 months ago by
jkbonfield • 400
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... I am assuming both files are chromosome / position sorted first, meaning the output will be too.
Are the two BAM files from different technologies? Compression tools such as gzip (the same algorithm is used exclusively in BAM) benefit from having similar looking data aggregated together. This is ...
written 8 months ago by
jkbonfield • 400
Latest awards to jkbonfield
Scholar
6 months ago,
created an answer that has been accepted.
For A: How does samtools markdup works?
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: What is the difference between mpileup samtools and bcftools?
Scholar
6 months ago,
created an answer that has been accepted.
For A: How does samtools markdup works?
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Recovering bam files after unknow deletion in the storage
Scholar
6 months ago,
created an answer that has been accepted.
For A: How does samtools markdup works?
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Recovering bam files after unknow deletion in the storage
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: Is it possible to directly convert fastq to CRAM ?
Good Answer
12 months ago,
created an answer that was upvoted at least 5 times.
For A: Is it possible to directly convert fastq to CRAM ?
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Recovering bam files after unknow deletion in the storage
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: what should a SAM/BAM record contain when there are no quality scores
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Recovering bam files after unknow deletion in the storage
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