Moderator: John Marshall
John Marshall ♦ 1.7k
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Posts by John Marshall
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3
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... “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 Marshall ♦ 1.7k
2
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2
answers
154
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2
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... 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 Marshall ♦ 1.7k
2
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4
answers
20k
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4
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... 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 Marshall ♦ 1.7k
1
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1
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127
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1
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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 Marshall ♦ 1.7k
1
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1
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361
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1
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... This spec infelicity is now . ...
written 12 weeks ago by
John Marshall ♦ 1.7k
0
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1
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148
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1
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... 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 Marshall ♦ 1.7k
1
vote
1
answer
361
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1
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... 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 Marshall ♦ 1.7k
6
votes
1
answer
361
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1
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... 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 Marshall ♦ 1.7k
1
vote
2
answers
164
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2
answers
... 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 Marshall ♦ 1.7k
0
votes
0
answers
19
views
0
answers
... 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 Marshall ♦ 1.7k
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2 days ago,
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For A: sam header is not recognized by awk?
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8 weeks ago,
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For A: SAMtools-1.2 sort options documentation
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12 weeks ago,
created a post with more than 5 votes.
For A: Duplicate @Sq Lines In Sam File Header
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For A: Duplicate @Sq Lines In Sam File Header
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For A: sam header is not recognized by awk?
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For A: SAMtools-1.2 sort options documentation
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For A: sam header is not recognized by awk?
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For A: Tool for random access to indexed BAM files in S3?
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