Moderator: finswimmer
finswimmer ♦ 13k
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Posts by finswimmer
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... Hello,
[bcftools reaheder](http://www.htslib.org/doc/bcftools.html#reheader) should help you here. To use it, you have to prepare a text file, where in each line you write the old and the new sample name. Or just the new sample name, but all names in the order they should appear in the vcf.
Then y ...
written 5 days ago by
finswimmer ♦ 13k
1
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1
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4.0k
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1
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Comment:
C: Sort VCF File by Position?
... `bcftools sort` is absolute the right way and the way I would go today :) ...
written 8 days ago by
finswimmer ♦ 13k
0
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1
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88
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1
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... Hello https://www.biostars.org/u/39092/,
this gives you a list of sequences:
```
domains = list(SeqIO.parse("domains.fa",'fasta'))
```
Later you try this
```
seq_n = domains.seq[0:num]
```
You have to define which element of the list you want to access, e.g.
```
seq_n = domains[0].seq[0:num]
` ...
written 9 days ago by
finswimmer ♦ 13k
1
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... Hm, do you have an example of your vcf file?
This works for me:
```
##fileformat=VCFv4.2
##contig=
##FORMAT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1
chr1 977330 rs2799066 T C 225 PASS . GT 0/1
chr1 977330 rs2799066 T C 225 PASS . GT 0/1
```
```
$ bcftools norm -D in.vcf
##fileformat=VCFv ...
written 11 days ago by
finswimmer ♦ 13k
0
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1
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93
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1
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... Shouldn't it be:
```
bcftools norm -D in.vcf -o out.vcf
```
(uppercase `D`)
? ...
written 11 days ago by
finswimmer ♦ 13k
1
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1
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90
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1
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Comment:
C: Fasta file not matching VCF
... Do you have insertions or deletions in your vcf? If so, then chr22:260034 in the consensus fasta will not represent the same position in the original fasta. ...
written 12 days ago by
finswimmer ♦ 13k
0
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... Hello https://www.biostars.org/u/41746/ ,
not an answer to your question, but why do you want to calculate the average base quality?
fin swimmer ...
written 15 days ago by
finswimmer ♦ 13k
0
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92
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... Hello https://www.biostars.org/u/48569/ ,
could you please add an example of your vcf including the header an some variant lines?
fin swimmer ...
written 22 days ago by
finswimmer ♦ 13k
0
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... Unless I've not missed an important point you can use `bcftools` to extract variant sites from a gvcfs
$ bcftools view -m2 input.vcf
The `-m` parameter filters for sites with a minimum number of alleles listed in REF and ALT. ...
written 28 days ago by
finswimmer ♦ 13k
1
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147
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... Is it of interest where the sequence align? Or is the question just "Do I have virus A and/or virus B" sequence in?
For the later one [bbduk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) might be helpful. See the usage example about "Kmer filtering". ...
written 6 weeks ago by
finswimmer ♦ 13k
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