User: sonia.olaechea
sonia.olaechea • 50
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Posts by sonia.olaechea
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C: update genotypes in vcf
... Okey, I'll try that, thanks! ...
written 8 days ago by
sonia.olaechea • 50
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C: update genotypes in vcf
... Okey, right, thanks :)!
But then, how do I change the genotypes? Still with my `sed` command?? Or somehow with Python? ...
written 8 days ago by
sonia.olaechea • 50
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... Hi all,
Recently, I've had some trouble with a VCF file in which a program had turn around my REF and ALT fields (e.g. REF=C, ALT=T, but should be REF=T, ALT=C) and also their related genotypes.
I've managed to turn around the REF and ALT fields, but I'm not able to update my genotypes in an effi ...
written 8 days ago by
sonia.olaechea • 50
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Comment:
C: Change ALT field in VCF
... head ALT.txt
rs10032042 G
rs10174691 C
rs10221923 G
rs10223644 G
rs1028771 C
rs10305678 G
rs10404081 G
rs10421281 C
rs1042478 G
rs10459252 C`
file ALT.txt
file ALT.txt: ASCII text`
...
written 13 days ago by
sonia.olaechea • 50
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... Hi all,
I have 2 vcf files for the same positions but with different individuals which I would like to merge.
However, in one of the files some of my variants have a `.` in the ALT field, which I would like to replace by the corresponding allele.
I've tried to obtain those alternatives alleles from ...
written 13 days ago by
sonia.olaechea • 50
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... Hi @finswimmer!
Yes, you were right, it hasn't worked :(
So, right now I'm trying to fix the REF alleles using `bcftools` plugin `+fixref`. I've launched this command:
bcftools +fixref myfile1.vcf.gz -- -f hg37.all.fa.gz
And it returns this output:
# SC, guessed strand convention
SC ...
written 27 days ago by
sonia.olaechea • 50
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... Hi again!
It turns out data `myfile1.vcf` comes from a chip and `myfile2.vcf` from a sequencing process (and it has been aligned afterwards)!! Both vcfs have as a reference hg19, but `myfile2.vcf' has more SNPs than the other file!
So I guess I will generate a list of the SNPs in `myfile1.vcf`, ext ...
written 28 days ago by
sonia.olaechea • 50
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... Oh, yes, we have a problem!
The only thing I can find in the header that could give us a clue is `##source:PLINKv1.90` and
`##INFO=` , what is actually not very informative, right'
By the way, I've tried changing the chromosomes names in the first column and it still gives an error, so I guess the ...
written 28 days ago by
sonia.olaechea • 50
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... Ouch! Newbies mistake hehe sorry! And I'll start by changing the chromosomes names, thank you very much!
Here are the contig lengths (lengths should be equal in both files right?) :
myfile1.vcf
`##contig=
##contig=
##contig=
##contig=
##contig=
##contig=
##contig= ...
written 28 days ago by
sonia.olaechea • 50
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... Hi @finswimmer,
one of my vcfs is kind of long (I have more than 1000 individuals), so I will omit their IDs and most of their genotypes okey? Also, both vcfs have a lot of header lines describing the contigs length, but I have removed them as well, else the comment will be too long. I've done this ...
written 28 days ago by
sonia.olaechea • 50
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