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Hi,
I'm writing to ask about an error which appeared to me when I ran VIVA for the first time.
I've ran the **command** below:
viva --vcf_file 450exomes-cohort_GENOTYPEGVCF.vcf --output_dir…
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Any plans on adding VCF, gVCF, GFF, BAM, SAM or others?
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Apologies for jumping into this discussion late. My question is what are the records in the intermediate VCF format? e.g. given two inputs
_Truth_
> 1 10 AT GT,AC 0/1
_Query_
> 1…
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vcf_reader = vcf.Reader(open(path,"r"), strict_whitespace=True)
vcf_writer = vcf.Writer(open(new.vcf, 'w'), vcf_reader, lineterminator='\n')
for record in vcf_reader:
vcf_writer.write_record(rec…
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Write a script to apply the user's filter selections to an annotated VCF.
Input parameters:
- _Filters_: command-line arguments describing the user's filter selections, e.g. "filters=clinsig:patho…
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In the Mapper module, supporting taking BAM input data and converting it to VCF output.
@dauss75, @chris-owen, this is one of the issues we discussed.
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```
As a one way automated copy feature, vcardio could autoimport all vcf
files in a certain predefind directory on start (or better -
periodically).
In conjuction with, for example, swiftp - ftp s…
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Hello- It seems that CAVA throws an exception if the input VCF file has no records. This is what I get:
```
cava.py -i in.vcf -c cava.config
----------------------------------------------------…
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Hi,
I was trying different window and buffer parameters, getting weird results. When I run chunk with `window-cm` and `window-mb` less equal 1, whatever `buffer-cm `and `buffer-mb` is, buffer is a…
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For some reason, when I generate reads using a VCF, most of the threads exit without a sound a few minutes after starting the thread. This seems to happen before the reads are assigned parts of the ge…