Moderator: John Marshall

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John Marshall1.7k
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Posts by John Marshall

<prev • 104 results • page 1 of 11 • next >
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Answer: A: Samtools view Exec format error Help
... “Exec format error” indicates that samtools has been unable to recognise the format of your file. Either you ran your bwa command with `nohup` or similar and somehow managed to get some binary characters into it, or there are some other commands you have not shown us that have replaced the file with ...
written 9 days ago by John Marshall1.7k
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Answer: A: Samtools view error when converting sam to bam file using sc-ATAC-seq data from
... What are the `1112:`, `1113:`, …, `678440:` at the start of the lines of the file you've showed us? They appear to be some kind of line numbers, and if they're really in the file then of course `samtools` will throw parse errors. If they're really in the file, you should figure out what in your pi ...
written 27 days ago by John Marshall1.7k
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Answer: A: Can You Please Tell Me Where I Find Information About .Fai File Format?
... HTSlib has provided a manual page describing this format for a few years now. See `man 5 faidx`, also on the web at [faidx(5) manual page](https://www.htslib.org/doc/faidx.html). ...
written 7 weeks ago by John Marshall1.7k
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Answer: A: Parsing tabix with pysam
... This message is specific to calling `fetch()` with no region given. From the pysam code: if region is None: if len(self.contigs) > 0: # when accessing a tabix file created prior tabix 1.0 # the full-file iterator is empty. raise ValueError( ...
written 8 weeks ago by John Marshall1.7k
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Comment: C: structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
... This spec infelicity is now . ...
written 12 weeks ago by John Marshall1.7k
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Answer: A: What are valid VCF symbolic alternate alleles for structural variants?
... Immediately after the text you've quoted, the rest of §1.4.5 says > **IUPAC ambiguity codes** > > Symbolic alleles can be used also to represent genuinely ambiguous data in VCF, for example: > > `##ALT=` > `##ALT=` So “The first level type must be one of the following” relates o ...
written 12 weeks ago by John Marshall1.7k
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Comment: C: structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
... To be sure, the spec doesn't give you any hint that this is important and used by the tools to construct indexes — sadly this is par for the course for this specification… ...
written 12 weeks ago by John Marshall1.7k
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Answer: A: structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
... 1) That says **should**, not **must**. To my reading, that means you can invent your own keywords as well, though it behooves you to describe them well. The text in the VCF 4.3 spec (which, once again, I recommend as being clearer and more detailed than the earlier documents) has > The reserved ...
written 12 weeks ago by John Marshall1.7k
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Answer: A: Having trouble with samtools cat
... Samtools cat does indeed have a `-b` option: it's for giving it a text file containing a list of the BAM filenames to be processed. You're giving it the BAM filenames directly on the command line, so should just give it the filenames — not via an option: samtools cat -h header.bam -o catR1.bam ...
written 12 weeks ago by John Marshall1.7k
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Comment: C: Type checker error with bedtools intersect
... That's not a BAM file. If you showed us the command used to make it, we would be able to guess at what format it actually is. ...
written 3 months ago by John Marshall1.7k

Latest awards to John Marshall

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 8 weeks ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Centurion 8 weeks ago, created 100 posts.
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Duplicate @Sq Lines In Sam File Header
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Duplicate @Sq Lines In Sam File Header
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 12 weeks ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Scholar 4 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Tool for random access to indexed BAM files in S3?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Scholar 11 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: SAM file: same reads ID, slightly different sequence
Appreciated 11 months ago, created a post with more than 5 votes. For A: Tool for random access to indexed BAM files in S3?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Scholar 11 months ago, created an answer that has been accepted. For A: SAMtools-1.2 sort options documentation
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: sam header is not recognized by awk?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Question about sam flags.
Scholar 2.0 years ago, created an answer that has been accepted. For A: Question about sam flags.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Question about sam flags.
Guru 2.3 years ago, received more than 100 upvotes.

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