User: jkbonfield
jkbonfield • 180
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Posts by jkbonfield
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Comment:
C: Merge bam files
... You should be using bcftools mpileup now as the samtools one is deprecated.
Also note you can specify multiple files directly with mpileup and they'll be merged in-situ as it processes them so there is no need to merge them manually. Eg:
bcftools mpileup -f reference.fa -o output.vcf file_1.b ...
written 24 days ago by
jkbonfield • 180
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... "samtools mpileup foo.bam" will produce the columns showing what bases are aligned at each position. The reference column will be N, but that's irrelevant if you want the consensus (unless you're planning on using imputation to use reference in zero coverage regions, which can be useful in some sit ...
written 25 days ago by
jkbonfield • 180
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... I'm unsure of precisely what you want, but chr:pos-pos returns all alignments that *overlap* pos and not all alignments *starting* at pos.
Your title implies you wanted the latter. If this is the case, I don't think such a tool exists but you could use mpileup to get a single coordinate and then c ...
written 25 days ago by
jkbonfield • 180
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... This seems like a very long-winded solution and doesn't apply if you don't have a reference to hand.
However that said, if you don't then your aligned BAM was probably aligned against a de-novo assembly and somewhere there should be a consensus lurking around.
I've generally done some trivial coun ...
written 25 days ago by
jkbonfield • 180
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Comment:
C: samtools flagstat calculation
... I don't understand your explanations: "various step dupemerge" could hide a multitude of sins! If you're using different pipelines and comparing the stats at the end then can see why flagstats would be different and I don't see why you'd assume samtools is the cause.
Flagstat is a very trivial alg ...
written 28 days ago by
jkbonfield • 180
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Comment:
C: .bam mpileup mapping quality
... The bit after the `^` in the sequence column is the mapping quality. You're referring to the next column which contains base qualities.
Note that that the mapping quality may have been modified by the BAQ algorithm (see `mpileup -B` option). ...
written 4 weeks ago by
jkbonfield • 180
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Answer:
A: .bam mpileup mapping quality
... The answer to this is both yes and no depending on interpretation of the question.
The mapping quality is only shown for the first base in the alignment, and if that base has been filtered out (e.g. due to use of the `-Q` option) then the corresponding `^x` part is also filtered out and it will no ...
written 4 weeks ago by
jkbonfield • 180
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... I have some old perl one-liner kicking around to do this from the samtools mpileup output, but it doesn't look like it'll handle multiple chromosomes. Likely it was a one-off hack for some task. Anyway maybe it can be adapted. Be warned: it's hideous! :-)
samtools mpileup in.bam | perl -ane ...
written 4 weeks ago by
jkbonfield • 180
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... Bzip2 is old, and besides bzip (aka bzip1) was better but was replaced because of now expired patent problems. The modern alternative to bzip2 is bsc (https://github.com/IlyaGrebnov/libbsc) and it totally owns bzip2. Very impresive work.
Also for sure you do get better compression with dedicated ...
written 9 weeks ago by
jkbonfield • 180
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... While CRAM is indeed much smaller than BAM, its primary benefit is when using aligned data so you can use a reference sequence (whether external or embedded). It does however still work without a reference.
I wouldn't recommend creating a fake reference just to get it to swallow things. You shou ...
written 3 months ago by
jkbonfield • 180
Latest awards to jkbonfield
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For A: Is it possible to directly convert fastq to CRAM ?
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3 months ago,
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For A: Is it possible to directly convert fastq to CRAM ?
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created an answer with at least 3 up-votes.
For A: Recovering bam files after unknow deletion in the storage
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For A: what should a SAM/BAM record contain when there are no quality scores
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For A: Recovering bam files after unknow deletion in the storage
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