User: steven.davis
steven.davis • 10
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- 5 months, 3 weeks ago
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- 2 years, 11 months ago
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Posts by steven.davis
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... What is the standard VCF INFO field, if any, to count the occurrences of variant genotypes having passed all filters?
Does AC count every occurrence of the alternate genotype, or only those occurrences where the call passes all filters?
Consider the haploid VCF snippet below. At position 300, the ...
written 7 months ago by
steven.davis • 10
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... @jrj.healey This is 15 months after your original post, but may help others. There is a maf2fasta.pl conversion script included with mugsy. How did you solve the conversion problem? ...
written 14 months ago by
steven.davis • 10
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... Thank you Pierre. I'm writing a Python module to parse the sequence ids and extract various data elements. I will put it on GitHub sometime soon. ...
written 2.6 years ago by
steven.davis • 10
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... What kind of instrument uses flowcells ending with BBXX? Here is the read sequence id line:
@ERR1417747.1 K00150:65:H77FVBBXX:7:1101:1570:1297 length=150 ...
written 2.6 years ago by
steven.davis • 10
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... Is there a way to extract instrument and flowcell from a read name like this:
>gnl|SRA|SRR1840614.1.1 FCC1KPRACXX:1:1101:1291:2172
FCC1KPRACXX : what is this?
1 = lane?
1101 = ?
1291 = x
2172 = y
I need to extract the flowcell if possible, so it can be assigned to reads ...
written 2.6 years ago by
steven.davis • 10
• updated
2.6 years ago by
Pierre Lindenbaum ♦ 123k
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... Solved it with help from a colleague. Problem solved with "--merge all" command line option. ...
written 2.9 years ago by
steven.davis • 10
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... I am merging multiple single-sample VCF files into one multi-sample VCF file with bcftools merge using this command:
bcftools merge --info-rules NS:sum -o outFilePath dir/*.gz
Previously, using bcftools 1.1, the output VCF file contained one row per position, like this:
#CHROM POS ID ...
written 2.9 years ago by
steven.davis • 10
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2.6 years ago,
created a question with more than 1,000 views.
For VCF output when merging with bcftools merge
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