User: jkbonfield

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jkbonfield490
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Posts by jkbonfield

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Comment: C: Converting CRAM slices to get a CRAM file
... I have no idea what a cram.slice file is. I've never heard of it! I assume someone has binary bisected CRAM on the slice boundaries, but that'd be just speculation. If you concatenate them together do you get a valid CRAM file that can be read by tools? ...
written 11 weeks ago by jkbonfield490
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Answer: A: Converting CRAM slices to get a CRAM file
... CRAM is it's own format rather than a derivation or improved version of BAM; much like BAM is a binary encoding of SAM, CRAM is just a different (smaller) binary encoding of SAM. Ignore the "slice" terminology as it's just confusing things. You simply need a program capable of reading CRAM and, if ...
written 11 weeks ago by jkbonfield490
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Answer: A: filter reads in BAM having a tag
... The `samtools view -d TAG in.bam` option will fix this for the next release. More generally we are also [working on][1] a generic filtering expression language which includes the same capability. Eg `samtools view -e '[SA] && rlen>qlen' would report reads only having an SA tag and where ...
written 3 months ago by jkbonfield490
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Answer: A: Read name not stored in CRAM file. Is it possible to create new read names for r
... See my reply to your question on github too. However I suspect this is a processing error somewhere else which has "baked in" the pregenerated names at some point, and then a merge or something has caused the collision. CRAM *does* track read-pairs even when the names are removed. However it's po ...
written 3 months ago by jkbonfield490
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Answer: A: What is the difference of output samtools depth and samtools view -c on location
... 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 12 months ago by jkbonfield490
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Comment: C: file size after sorting the BAM file using samtools
... 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 12 months ago by jkbonfield490
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Comment: C: Collapsing BAM based on seq and positions
... 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 13 months ago by jkbonfield490
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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 13 months ago by jkbonfield490 • updated 13 months ago by Ram32k
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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 13 months ago by jkbonfield490
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Answer: A: What is the difference between mpileup samtools and bcftools?
... `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 13 months ago by jkbonfield490

Latest awards to jkbonfield

Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Is it possible to directly convert fastq to CRAM ?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Is it possible to directly convert fastq to CRAM ?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Recovering bam files after unknow deletion in the storage
Scholar 13 months ago, created an answer that has been accepted. For A: How does samtools markdup works?
Appreciated 13 months ago, created a post with more than 5 votes. For A: What is the difference between mpileup samtools and bcftools?
Scholar 13 months ago, created an answer that has been accepted. For A: How does samtools markdup works?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Recovering bam files after unknow deletion in the storage
Scholar 14 months ago, created an answer that has been accepted. For A: How does samtools markdup works?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Recovering bam files after unknow deletion in the storage
Appreciated 20 months ago, created a post with more than 5 votes. For A: Is it possible to directly convert fastq to CRAM ?
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Is it possible to directly convert fastq to CRAM ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Recovering bam files after unknow deletion in the storage
Teacher 20 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 21 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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