User: User000

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User000290
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Posts by User000

<prev • 264 results • page 1 of 27 • next >
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Comment: C: Freebayes variant calling understanding
... thank you Kevin, I still haven't found a solution for the second part of my question, but if you want to close the thread, go ahead. ...
written 20 days ago by User000290
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Answer: C: Extract several columns from a VCF file
... Yes, now I found a solution: bcftools view -S in.txt in.vcf > out.vcf If you were polite and just wrote your latest comment, we would have avoided upsetting each other. Don't take for granted that understanding some concepts are easy for everybody like they are for you. Sometimes we just ne ...
written 24 days ago by User000290
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Comment: C: Extract several columns from a VCF file
... I wouldn't be asking questions here if I wasn't stuck. So sorry I am not as brilliant as you are! Also, if you are not willing to help, just do not comment, as I am a grown up person and I know how to study! thanks ...
written 24 days ago by User000290
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Comment: C: Extract several columns from a VCF file
... vcf format #header1 #header2 #etc #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ID1 ID2 ID3 ID4 ID5...ID100 I need to get some of this ID's ...
written 24 days ago by User000290
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Comment: C: Extract several columns from a VCF file
... a bit more details would be much appreciated, as I studied it, but without any success. ...
written 24 days ago by User000290
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Extract several columns from a VCF file
... Hello, I have a vcf file with 100 genotypes. I want to extract information on 10 specific genotypes and I have a list of their ID's. Any ideas which tool could be used? ...
vcf written 24 days ago by User000290 • updated 19 days ago by omid.alavijeh40
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Freebayes adjusting parameters to "force" homozygous call
... How to change the freebayes parameters in following situations: Even if there is only one reference allele with a high mapping quality 60 freebayes would result in a 0/1 call. For me this could be an alternative allele. Any suggestions? [image here][1] [1]: https://ibb.co/album/hUsYAa ...
variant calling freebayes written 26 days ago by User000290
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Comment: C: Freebayes variant calling understanding
... Ah I see, so you mean the allele is different from other genotypes! ...
written 26 days ago by User000290
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Comment: C: Freebayes variant calling understanding
... that sounds reasonable, but when I have a look at the loci in bam file, I can see only reference allele and alternative allele, something like this: [image here][1] [1]: https://ibb.co/album/duefqa ...
written 26 days ago by User000290
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Freebayes variant calling understanding
... Hello, I am using freebayes to do variant calling in my polyploid species (with ploidy 2 anyway). Before filtering I was looking at the bam file alignment and a vcf file. Could you, please explain what does alleles `2/2, 0/2, 1/2` means? `0/0` is reference allele, `1/1` alternative and `0/1` hetero ...
freebayes snp written 26 days ago by User000290

Latest awards to User000

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